data_4MS9

loop_
_pdbx_vrpt_database.id
_pdbx_vrpt_database.code
PDB  4MS9    
NDB  NA2738  
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    4MS9
_pdbx_vrpt_summary.PDB_deposition_date         2013-09-18
_pdbx_vrpt_summary.PDB_revision_number         5
_pdbx_vrpt_summary.PDB_revision_date           2024-02-28
_pdbx_vrpt_summary.RNA_suiteness               0.86
_pdbx_vrpt_summary.report_creation_date        2024-02-20:17:36
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,mogul,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "Native RNA duplex 10mer"  
2  non-polymer  "STRONTIUM ION"  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  2  
D  2  
E  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  1.32  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore    
2  RSRZ_outliers_percent  
3  R_value_R_free         
4  RNAsuiteness_percent   
#
loop_
_pdbx_vrpt_percentile_conditions.id
_pdbx_vrpt_percentile_conditions.percentile_list_id
_pdbx_vrpt_percentile_conditions.type_id
_pdbx_vrpt_percentile_conditions.rank
_pdbx_vrpt_percentile_conditions.number_entries_total
_pdbx_vrpt_percentile_conditions.res_high
_pdbx_vrpt_percentile_conditions.res_low
1  1  1   99.96  141614     ?     ?  
2  2  1   99.94    1667  1.30  1.34  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    1580  1.30  1.34  
5  1  3   57.97  130704     ?     ?  
6  2  3    7.13    1611  1.30  1.34  
7  1  4   97.97    3102     ?     ?  
8  2  4   94.10    1000  0.62  2.34  
#
loop_
_pdbx_vrpt_percentile_entity_view.ordinal
_pdbx_vrpt_percentile_entity_view.conditions_id
_pdbx_vrpt_percentile_entity_view.type_id
_pdbx_vrpt_percentile_entity_view.label_asym_id
_pdbx_vrpt_percentile_entity_view.PDB_model_num
_pdbx_vrpt_percentile_entity_view.entity_id
_pdbx_vrpt_percentile_entity_view.auth_asym_id
_pdbx_vrpt_percentile_entity_view.rank
1  3  2  A  1  1  A  100.00  
2  4  2  A  1  1  A  100.00  
#
_pdbx_vrpt_summary_entity_geometry.ordinal          1
_pdbx_vrpt_summary_entity_geometry.PDB_model_num    1
_pdbx_vrpt_summary_entity_geometry.entity_id        1
_pdbx_vrpt_summary_entity_geometry.label_asym_id    A
_pdbx_vrpt_summary_entity_geometry.auth_asym_id     A
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ      1.03
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       1.07
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   236
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  367
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       0.00
_pdbx_vrpt_summary_geometry.num_H_reduce     110
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   236
_pdbx_vrpt_summary_geometry.bonds_RMSZ       1.07
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  367
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.03
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 261.673
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            56.916
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         12.699
_pdbx_vrpt_summary_diffraction.I_over_sigma              49.99(1.32A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        5718
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.121
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.354
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.497
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.330
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.960
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,-k,l:0.058
_pdbx_vrpt_summary_diffraction.DCC_R                     0.19
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.23
_pdbx_vrpt_summary_diffraction.EDS_R                     0.19
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.32
_pdbx_vrpt_summary_diffraction.EDS_res_low               19.06
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[13.225,13.225,11.383,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.146
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 14.29% of the height of the origin peak. No significant pseudotranslation is detected."
_pdbx_vrpt_summary_diffraction.B_factor_type             FULL
_pdbx_vrpt_summary_diffraction.acentric_outliers         0
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         97.10
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      256
_pdbx_vrpt_summary_diffraction.percent_free_reflections  4.48
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.32
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        25.91
_pdbx_vrpt_summary_diffraction.PDB_R                     0.19
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.23
#
loop_
_pdbx_vrpt_model_instance.id
_pdbx_vrpt_model_instance.PDB_model_num
_pdbx_vrpt_model_instance.entity_id
_pdbx_vrpt_model_instance.label_asym_id
_pdbx_vrpt_model_instance.label_seq_id
_pdbx_vrpt_model_instance.label_comp_id
_pdbx_vrpt_model_instance.auth_asym_id
_pdbx_vrpt_model_instance.auth_seq_id
_pdbx_vrpt_model_instance.label_alt_id
_pdbx_vrpt_model_instance.PDB_ins_code
_pdbx_vrpt_model_instance.count_bond_outliers
 1  1  1  A   1  C    A    1  .  ?        ?  
 2  1  1  A   2  C    A    2  .  ?        ?  
 3  1  1  A   3  G    A    3  .  ?        ?  
 4  1  1  A   4  G    A    4  .  ?        ?  
 5  1  1  A   5  C    A    5  .  ?        ?  
 6  1  1  A   6  G    A    6  .  ?        ?  
 7  1  1  A   7  C    A    7  .  ?        ?  
 8  1  1  A   8  C    A    8  .  ?        ?  
 9  1  1  A   9  G    A    9  .  ?        1  
10  1  1  A  10  G    A   10  .  ?        ?  
11  1  2  B   .  SR   A  101  .  ?        ?  
12  1  2  C   .  SR   A  102  .  ?        ?  
13  1  2  D   .  SR   A  103  .  ?        ?  
14  1  3  E   .  HOH  A  201  .  ?        ?  
15  1  3  E   .  HOH  A  202  .  ?        ?  
16  1  3  E   .  HOH  A  203  .  ?        ?  
17  1  3  E   .  HOH  A  204  .  ?        ?  
18  1  3  E   .  HOH  A  205  .  ?        ?  
19  1  3  E   .  HOH  A  206  .  ?        ?  
20  1  3  E   .  HOH  A  207  .  ?        ?  
21  1  3  E   .  HOH  A  208  .  ?        ?  
22  1  3  E   .  HOH  A  209  .  ?        ?  
23  1  3  E   .  HOH  A  210  .  ?        ?  
24  1  3  E   .  HOH  A  211  .  ?        ?  
25  1  3  E   .  HOH  A  212  .  ?        ?  
26  1  3  E   .  HOH  A  213  .  ?        ?  
27  1  3  E   .  HOH  A  214  .  ?        ?  
28  1  3  E   .  HOH  A  215  .  ?        ?  
29  1  3  E   .  HOH  A  216  .  ?        ?  
30  1  3  E   .  HOH  A  217  .  ?        ?  
31  1  3  E   .  HOH  A  218  .  ?        ?  
32  1  3  E   .  HOH  A  219  .  ?        ?  
33  1  3  E   .  HOH  A  220  .  ?        ?  
34  1  3  E   .  HOH  A  221  .  ?        ?  
35  1  3  E   .  HOH  A  222  .  ?        ?  
36  1  3  E   .  HOH  A  223  .  ?        ?  
37  1  3  E   .  HOH  A  224  .  ?        ?  
38  1  3  E   .  HOH  A  225  .  ?        ?  
39  1  3  E   .  HOH  A  226  .  ?        ?  
40  1  3  E   .  HOH  A  227  .  ?        ?  
41  1  3  E   .  HOH  A  228  .  ?        ?  
42  1  3  E   .  HOH  A  229  .  ?        ?  
43  1  3  E   .  HOH  A  230  .  ?        ?  
44  1  3  E   .  HOH  A  231  .  ?        ?  
45  1  3  E   .  HOH  A  232  .  ?        ?  
46  1  3  E   .  HOH  A  233  .  ?        ?  
47  1  3  E   .  HOH  A  234  .  ?        ?  
48  1  3  E   .  HOH  A  235  .  ?        ?  
49  1  3  E   .  HOH  A  236  .  ?        ?  
50  1  3  E   .  HOH  A  237  .  ?        ?  
51  1  3  E   .  HOH  A  238  .  ?        ?  
52  1  3  E   .  HOH  A  239  .  ?        ?  
53  1  3  E   .  HOH  A  240  .  ?        ?  
54  1  3  E   .  HOH  A  241  .  ?        ?  
55  1  3  E   .  HOH  A  242  .  ?        ?  
56  1  3  E   .  HOH  A  243  .  ?        ?  
57  1  3  E   .  HOH  A  244  .  ?        ?  
58  1  3  E   .  HOH  A  245  .  ?        ?  
59  1  3  E   .  HOH  A  246  .  ?        ?  
60  1  3  E   .  HOH  A  247  .  ?        ?  
61  1  3  E   .  HOH  A  248  .  ?        ?  
62  1  3  E   .  HOH  A  249  .  ?        ?  
63  1  3  E   .  HOH  A  250  .  ?        ?  
64  1  3  E   .  HOH  A  251  .  ?        ?  
65  1  3  E   .  HOH  A  252  .  ?        ?  
66  1  3  E   .  HOH  A  253  .  ?        ?  
67  1  3  E   .  HOH  A  254  .  ?        ?  
68  1  3  E   .  HOH  A  255  .  ?        ?  
69  1  3  E   .  HOH  A  256  .  ?        ?  
70  1  3  E   .  HOH  A  257  .  ?        ?  
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.RNA_score
_pdbx_vrpt_model_instance_geometry.RNA_suite
_pdbx_vrpt_model_instance_geometry.num_H_reduce
_pdbx_vrpt_model_instance_geometry.OWAB
_pdbx_vrpt_model_instance_geometry.num_bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.num_angles_RMSZ
_pdbx_vrpt_model_instance_geometry.angles_RMSZ
_pdbx_vrpt_model_instance_geometry.program_for_bond_angle_geometry
_pdbx_vrpt_model_instance_geometry.average_occupancy
 1   1  0.00  NotAvailable    12  24.720    19  0.90    30  0.54  molprobity  1.000  
 2   2  0.66  Rotameric       11  14.040    22  1.09    34  1.10  molprobity  1.000  
 3   3  0.87  Rotameric       11  10.820    26  0.91    41  0.98  molprobity  1.000  
 4   4  0.89  Rotameric       11  11.040    26  0.73    41  0.98  molprobity  1.000  
 5   5  0.83  Rotameric       11  11.500    22  0.89    34  1.01  molprobity  1.000  
 6   6  0.85  Rotameric       11  13.250    26  1.24    41  0.82  molprobity  1.000  
 7   7  0.87  Rotameric       11  12.650    22  1.09    34  1.17  molprobity  1.000  
 8   8  0.85  Rotameric       11  12.200    22  1.39    34  1.24  molprobity  1.000  
 9   9  0.97  Rotameric       11  13.010    26  1.50    41  1.17  molprobity  1.000  
10  10  0.94  Rotameric       10  18.360    25  0.51    37  1.05  molprobity  1.000  
11  11     ?  ?                ?  13.450     ?     ?     ?     ?  ?           0.650  
12  12     ?  ?                ?  16.600     ?     ?     ?     ?  ?           0.400  
13  13     ?  ?                ?  17.270     ?     ?     ?     ?  ?           0.400  
14  14     ?  ?                ?  13.650     ?     ?     ?     ?  ?           1.000  
15  15     ?  ?                ?  16.970     ?     ?     ?     ?  ?           1.000  
16  16     ?  ?                ?  23.080     ?     ?     ?     ?  ?           1.000  
17  17     ?  ?                ?  18.260     ?     ?     ?     ?  ?           1.000  
18  18     ?  ?                ?  15.430     ?     ?     ?     ?  ?           1.000  
19  19     ?  ?                ?  15.300     ?     ?     ?     ?  ?           1.000  
20  20     ?  ?                ?  16.700     ?     ?     ?     ?  ?           1.000  
21  21     ?  ?                ?  18.830     ?     ?     ?     ?  ?           1.000  
22  22     ?  ?                ?  25.180     ?     ?     ?     ?  ?           1.000  
23  23     ?  ?                ?  32.630     ?     ?     ?     ?  ?           1.000  
24  24     ?  ?                ?  26.420     ?     ?     ?     ?  ?           1.000  
25  25     ?  ?                ?  19.870     ?     ?     ?     ?  ?           1.000  
26  26     ?  ?                ?  18.070     ?     ?     ?     ?  ?           1.000  
27  27     ?  ?                ?  22.940     ?     ?     ?     ?  ?           1.000  
28  28     ?  ?                ?  23.070     ?     ?     ?     ?  ?           1.000  
29  29     ?  ?                ?  25.050     ?     ?     ?     ?  ?           1.000  
30  30     ?  ?                ?  22.910     ?     ?     ?     ?  ?           1.000  
31  31     ?  ?                ?  22.140     ?     ?     ?     ?  ?           1.000  
32  32     ?  ?                ?  31.540     ?     ?     ?     ?  ?           1.000  
33  33     ?  ?                ?  19.720     ?     ?     ?     ?  ?           1.000  
34  34     ?  ?                ?  20.100     ?     ?     ?     ?  ?           1.000  
35  35     ?  ?                ?  24.460     ?     ?     ?     ?  ?           1.000  
36  36     ?  ?                ?  28.490     ?     ?     ?     ?  ?           1.000  
37  37     ?  ?                ?  24.140     ?     ?     ?     ?  ?           1.000  
38  38     ?  ?                ?  26.230     ?     ?     ?     ?  ?           1.000  
39  39     ?  ?                ?  13.480     ?     ?     ?     ?  ?           1.000  
40  40     ?  ?                ?  16.780     ?     ?     ?     ?  ?           1.000  
41  41     ?  ?                ?  35.200     ?     ?     ?     ?  ?           1.000  
42  42     ?  ?                ?  24.910     ?     ?     ?     ?  ?           1.000  
43  43     ?  ?                ?  27.830     ?     ?     ?     ?  ?           1.000  
44  44     ?  ?                ?  24.650     ?     ?     ?     ?  ?           1.000  
45  45     ?  ?                ?  21.800     ?     ?     ?     ?  ?           1.000  
46  46     ?  ?                ?  20.000     ?     ?     ?     ?  ?           1.000  
47  47     ?  ?                ?  29.850     ?     ?     ?     ?  ?           1.000  
48  48     ?  ?                ?  21.940     ?     ?     ?     ?  ?           1.000  
49  49     ?  ?                ?  19.220     ?     ?     ?     ?  ?           1.000  
50  50     ?  ?                ?  20.130     ?     ?     ?     ?  ?           1.000  
51  51     ?  ?                ?  34.770     ?     ?     ?     ?  ?           1.000  
52  52     ?  ?                ?  28.510     ?     ?     ?     ?  ?           1.000  
53  53     ?  ?                ?  22.950     ?     ?     ?     ?  ?           1.000  
54  54     ?  ?                ?  30.240     ?     ?     ?     ?  ?           1.000  
55  55     ?  ?                ?  34.750     ?     ?     ?     ?  ?           1.000  
56  56     ?  ?                ?  30.650     ?     ?     ?     ?  ?           1.000  
57  57     ?  ?                ?  30.350     ?     ?     ?     ?  ?           1.000  
58  58     ?  ?                ?  13.600     ?     ?     ?     ?  ?           1.000  
59  59     ?  ?                ?  30.460     ?     ?     ?     ?  ?           1.000  
60  60     ?  ?                ?  26.680     ?     ?     ?     ?  ?           1.000  
61  61     ?  ?                ?  15.540     ?     ?     ?     ?  ?           1.000  
62  62     ?  ?                ?  25.560     ?     ?     ?     ?  ?           1.000  
63  63     ?  ?                ?  38.690     ?     ?     ?     ?  ?           1.000  
64  64     ?  ?                ?  22.170     ?     ?     ?     ?  ?           1.000  
65  65     ?  ?                ?  34.610     ?     ?     ?     ?  ?           1.000  
66  66     ?  ?                ?  18.760     ?     ?     ?     ?  ?           0.500  
67  67     ?  ?                ?  34.390     ?     ?     ?     ?  ?           1.000  
68  68     ?  ?                ?  28.120     ?     ?     ?     ?  ?           1.000  
69  69     ?  ?                ?  30.990     ?     ?     ?     ?  ?           1.000  
70  70     ?  ?                ?   5.440     ?     ?     ?     ?  ?           0.500  
#
_pdbx_vrpt_instance_intra_bond_outliers.ordinal      1
_pdbx_vrpt_instance_intra_bond_outliers.instance_id  9
_pdbx_vrpt_instance_intra_bond_outliers.atom_1       P
_pdbx_vrpt_instance_intra_bond_outliers.atom_2       OP2
_pdbx_vrpt_instance_intra_bond_outliers.obs          1.382
_pdbx_vrpt_instance_intra_bond_outliers.mean         1.485
_pdbx_vrpt_instance_intra_bond_outliers.stdev        0.017
_pdbx_vrpt_instance_intra_bond_outliers.Z            -6.04
#
loop_
_pdbx_vrpt_model_instance_density.ordinal
_pdbx_vrpt_model_instance_density.instance_id
_pdbx_vrpt_model_instance_density.natoms_eds
_pdbx_vrpt_model_instance_density.RSRCC
_pdbx_vrpt_model_instance_density.RSR
_pdbx_vrpt_model_instance_density.RSRZ
 1   1  17  0.914  0.125   1.096  
 2   2  20  0.977  0.052  -0.743  
 3   3  23  0.980  0.054  -0.693  
 4   4  23  0.978  0.058  -0.595  
 5   5  20  0.979  0.056  -0.642  
 6   6  23  0.974  0.062  -0.498  
 7   7  20  0.971  0.060  -0.542  
 8   8  20  0.959  0.071  -0.264  
 9   9  23  0.973  0.057  -0.620  
10  10  23  0.943  0.080  -0.059  
11  11   1  0.987  0.038       ?  
12  12   1  0.981  0.044       ?  
13  13   1  0.945  0.068       ?  
14  14   1  0.988  0.070       ?  
15  15   1  0.980  0.083       ?  
16  16   1  0.950  0.080       ?  
17  17   1  0.956  0.067       ?  
18  18   1  0.964  0.105       ?  
19  19   1  0.990  0.057       ?  
20  20   1  0.969  0.109       ?  
21  21   1  0.983  0.079       ?  
22  22   1  0.893  0.120       ?  
23  23   1  0.845  0.135       ?  
24  24   1  0.908  0.131       ?  
25  25   1  0.954  0.099       ?  
26  26   1  0.975  0.063       ?  
27  27   1  0.918  0.126       ?  
28  28   1  0.972  0.147       ?  
29  29   1  0.896  0.129       ?  
30  30   1  0.941  0.111       ?  
31  31   1  0.898  0.115       ?  
32  32   1  0.751  0.139       ?  
33  33   1  0.950  0.067       ?  
34  34   1  0.957  0.079       ?  
35  35   1  0.950  0.109       ?  
36  36   1  0.874  0.242       ?  
37  37   1  0.935  0.184       ?  
38  38   1  0.922  0.075       ?  
39  39   1  0.935  0.130       ?  
40  40   1  0.973  0.048       ?  
41  41   1  0.852  0.151       ?  
42  42   1  0.911  0.149       ?  
43  43   1  0.885  0.257       ?  
44  44   1  0.929  0.130       ?  
45  45   1  0.944  0.076       ?  
46  46   1  0.972  0.066       ?  
47  47   1  0.904  0.201       ?  
48  48   1  0.968  0.086       ?  
49  49   1  0.962  0.127       ?  
50  50   1  0.964  0.082       ?  
51  51   1  0.831  0.125       ?  
52  52   1  0.849  0.132       ?  
53  53   1  0.973  0.208       ?  
54  54   1  0.837  0.132       ?  
55  55   1  0.737  0.274       ?  
56  56   1  0.848  0.167       ?  
57  57   1  0.740  0.354       ?  
58  58   1  0.990  0.063       ?  
59  59   1  0.822  0.126       ?  
60  60   1  0.804  0.161       ?  
61  61   1  0.979  0.135       ?  
62  62   1  0.912  0.094       ?  
63  63   1  0.747  0.200       ?  
64  64   1  0.877  0.102       ?  
65  65   1  0.792  0.193       ?  
66  66   1  0.971  0.063       ?  
67  67   1  0.650  0.135       ?  
68  68   1  0.872  0.126       ?  
69  69   1  0.898  0.114       ?  
70  70   1  0.994  0.095       ?  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity   4.02b-467                                                             Y  
2  mogul        unknown                                                               Y  
3  eds          2.36                                                                  Y  
4  dcc          '"2.27  (2023-04-10)"'                                                Y  
5  xtriage      1.13                                                                  Y  
6  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
