data_1Y3O

loop_
_pdbx_vrpt_database.id
_pdbx_vrpt_database.code
PDB  1Y3O    
NDB  UR0049  
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    1Y3O
_pdbx_vrpt_summary.PDB_deposition_date         2004-11-26
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2023-08-23
_pdbx_vrpt_summary.RNA_suiteness               0.79
_pdbx_vrpt_summary.report_creation_date        2023-08-15:13:20
_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      "5'-R(*CP*UP*(5BU)P*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3'"  
2  non-polymer  "MANGANESE (II) ION"  
3  non-polymer  "SODIUM ION"  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  2  
D  2  
E  2  
F  3  
G  2  
H  3  
I  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  2.7  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   72.18  141614     ?     ?  
2  2  1   86.13    3122  2.70  2.70  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    2737  2.70  2.70  
5  1  3   12.99  130704     ?     ?  
6  2  3   28.64    2808  2.70  2.70  
7  1  4   93.42    3102     ?     ?  
8  2  4   97.84    1159  2.40  3.00  
#
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  
3  3  2  B  1  1  B  100.00  
4  4  2  B  1  1  B  100.00  
#
loop_
_pdbx_vrpt_summary_entity_geometry.ordinal
_pdbx_vrpt_summary_entity_geometry.PDB_model_num
_pdbx_vrpt_summary_entity_geometry.entity_id
_pdbx_vrpt_summary_entity_geometry.label_asym_id
_pdbx_vrpt_summary_entity_geometry.auth_asym_id
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ
1  1  1  A  A  0.66  0.52  525  817  
2  1  1  B  B  0.66  0.56  525  817  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       3.36
_pdbx_vrpt_summary_geometry.num_H_reduce     500
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   1050
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.54
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1634
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.66
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 142.756
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            27.097
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         57.332
_pdbx_vrpt_summary_diffraction.I_over_sigma              2.77(2.72A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        7784
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.265
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.210
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.488
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.325
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.949
_pdbx_vrpt_summary_diffraction.DCC_R                     0.22
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.28
_pdbx_vrpt_summary_diffraction.EDS_R                     0.23
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.70
_pdbx_vrpt_summary_diffraction.EDS_res_low               28.02
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[55.219,38.134,105.455,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           1.016
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 28.22 % of the origin peak, indicating pseudo-translational symmetry.  The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 1.9138e-03. The detected translational NCS is most likely also responsible for the elevated intensity ratio.  See the relevant section of the logfile for more details."
_pdbx_vrpt_summary_diffraction.B_factor_type             FULL
_pdbx_vrpt_summary_diffraction.acentric_outliers         17
_pdbx_vrpt_summary_diffraction.centric_outliers          6
_pdbx_vrpt_summary_diffraction.data_completeness         97.68
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      792
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.17
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.70
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        10.00
_pdbx_vrpt_summary_diffraction.PDB_R                     0.22
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.28
#
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_clashes
 1  1  1  A   1  C    A    1  .  ?        ?  
 2  1  1  A   2  U    A    2  .  ?        ?  
 3  1  1  A   3  5BU  A    3  .  ?        ?  
 4  1  1  A   4  G    A    4  .  ?        ?  
 5  1  1  A   5  C    A    5  .  ?        ?  
 6  1  1  A   6  U    A    6  .  ?        2  
 7  1  1  A   7  G    A    7  .  ?        2  
 8  1  1  A   8  A    A    8  .  ?        ?  
 9  1  1  A   9  A    A    9  .  ?        ?  
10  1  1  A  10  G    A   10  .  ?        ?  
11  1  1  A  11  U    A   11  .  ?        ?  
12  1  1  A  12  G    A   12  .  ?        1  
13  1  1  A  13  C    A   13  .  ?        1  
14  1  1  A  14  A    A   14  .  ?        ?  
15  1  1  A  15  C    A   15  .  ?        ?  
16  1  1  A  16  A    A   16  .  ?        ?  
17  1  1  A  17  C    A   17  .  ?        ?  
18  1  1  A  18  A    A   18  .  ?        ?  
19  1  1  A  19  G    A   19  .  ?        ?  
20  1  1  A  20  C    A   20  .  ?        ?  
21  1  1  A  21  A    A   21  .  ?        ?  
22  1  1  A  22  A    A   22  .  ?        ?  
23  1  1  A  23  G    A   23  .  ?        ?  
24  1  1  B   1  C    B    1  .  ?        ?  
25  1  1  B   2  U    B    2  .  ?        ?  
26  1  1  B   3  5BU  B    3  .  ?        ?  
27  1  1  B   4  G    B    4  .  ?        ?  
28  1  1  B   5  C    B    5  .  ?        ?  
29  1  1  B   6  U    B    6  .  ?        2  
30  1  1  B   7  G    B    7  .  ?        2  
31  1  1  B   8  A    B    8  .  ?        ?  
32  1  1  B   9  A    B    9  .  ?        ?  
33  1  1  B  10  G    B   10  .  ?        ?  
34  1  1  B  11  U    B   11  .  ?        ?  
35  1  1  B  12  G    B   12  .  ?        ?  
36  1  1  B  13  C    B   13  .  ?        ?  
37  1  1  B  14  A    B   14  .  ?        ?  
38  1  1  B  15  C    B   15  .  ?        ?  
39  1  1  B  16  A    B   16  .  ?        ?  
40  1  1  B  17  C    B   17  .  ?        ?  
41  1  1  B  18  A    B   18  .  ?        ?  
42  1  1  B  19  G    B   19  .  ?        ?  
43  1  1  B  20  C    B   20  .  ?        ?  
44  1  1  B  21  A    B   21  .  ?        ?  
45  1  1  B  22  A    B   22  .  ?        ?  
46  1  1  B  23  G    B   23  .  ?        ?  
47  1  2  C   .  MN   A  100  .  ?        ?  
48  1  2  D   .  MN   A  102  .  ?        ?  
49  1  2  E   .  MN   A  103  .  ?        ?  
50  1  3  F   .  NA   A  105  .  ?        ?  
51  1  2  G   .  MN   B  101  .  ?        ?  
52  1  3  H   .  NA   B  104  .  ?        ?  
53  1  3  I   .  NA   B  106  .  ?        ?  
#
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  47.960    19  0.47    30  0.50  molprobity  1.000  
 2   2  0.57  Rotameric       10  48.500    21  0.70    30  0.57  molprobity  1.000  
 3   3  0.88  Rotameric        9  54.600    19  0.46    28  0.53  mogul       0.969  
 4   4  0.91  Rotameric       11  51.100    26  0.37    41  0.67  molprobity  1.000  
 5   5  0.85  Rotameric       11  61.080    22  0.48    34  0.51  molprobity  1.000  
 6   6  0.94  Rotameric       10  60.680    22  0.33    34  0.66  molprobity  1.000  
 7   7  0.61  Rotameric       11  59.300    26  0.45    41  0.73  molprobity  1.000  
 8   8  0.14  Rotameric       11  54.950    25  0.52    39  0.82  molprobity  1.000  
 9   9  0.63  Rotameric       11  47.930    25  0.36    39  0.76  molprobity  1.000  
10  10  0.70  Rotameric       11  55.910    26  0.45    41  0.51  molprobity  1.000  
11  11  0.89  Rotameric       10  56.650    22  0.65    34  0.69  molprobity  1.000  
12  12  0.88  Rotameric       11  53.410    26  0.49    41  0.55  molprobity  1.000  
13  13  0.74  Rotameric       11  51.330    22  0.85    34  0.60  molprobity  1.000  
14  14  0.91  Rotameric       11  51.340    25  0.81    39  0.59  molprobity  1.000  
15  15  0.87  Rotameric       11  52.670    22  0.50    34  0.58  molprobity  1.000  
16  16  0.96  Rotameric       11  57.550    25  0.44    39  0.62  molprobity  1.000  
17  17  0.83  Rotameric       11  66.640    22  0.41    34  0.73  molprobity  1.000  
18  18  0.82  Rotameric       11  61.870    25  0.44    39  0.53  molprobity  1.000  
19  19  0.94  Rotameric       11  64.100    26  0.56    41  0.67  molprobity  1.000  
20  20  0.90  Rotameric       11  70.690    22  0.45    34  0.70  molprobity  1.000  
21  21  0.70  Rotameric       11  65.180    25  0.50    39  0.72  molprobity  1.000  
22  22  0.44  Rotameric       11  63.310    25  0.38    39  0.96  molprobity  1.000  
23  23  0.82  Rotameric       12  51.720    25  0.46    37  0.60  molprobity  1.000  
24  24  0.00  NotAvailable    12  52.010    19  0.44    30  0.42  molprobity  1.000  
25  25  0.33  Rotameric       10  52.470    21  0.82    30  0.63  molprobity  1.000  
26  26  0.97  Rotameric        9  51.600    19  0.58    28  0.55  mogul       0.968  
27  27  0.82  Rotameric       11  53.000    26  0.49    41  0.67  molprobity  1.000  
28  28  0.94  Rotameric       11  57.170    22  0.46    34  0.70  molprobity  1.000  
29  29  0.84  Rotameric       10  59.970    22  0.90    34  0.58  molprobity  1.000  
30  30  0.88  Rotameric       11  58.670    26  0.49    41  0.65  molprobity  1.000  
31  31  0.74  Rotameric       11  50.150    25  0.45    39  0.78  molprobity  1.000  
32  32  0.70  Rotameric       11  50.790    25  0.58    39  0.57  molprobity  1.000  
33  33  0.02  Rotameric       11  60.790    26  0.52    41  0.56  molprobity  1.000  
34  34  0.87  Rotameric       10  64.530    22  0.50    34  0.73  molprobity  1.000  
35  35  0.95  Rotameric       11  58.070    26  0.69    41  0.45  molprobity  1.000  
36  36  0.90  Rotameric       11  60.230    22  0.59    34  0.77  molprobity  1.000  
37  37  0.89  Rotameric       11  50.060    25  0.72    39  0.74  molprobity  1.000  
38  38  0.94  Rotameric       11  52.660    22  0.50    34  0.83  molprobity  1.000  
39  39  0.78  Rotameric       11  55.240    25  0.47    39  0.69  molprobity  1.000  
40  40  0.97  Rotameric       11  62.570    22  0.56    34  0.71  molprobity  1.000  
41  41  0.99  Rotameric       11  58.770    25  0.33    39  0.71  molprobity  1.000  
42  42  0.63  Rotameric       11  63.390    26  0.30    41  0.60  molprobity  1.000  
43  43  0.94  Rotameric       11  63.830    22  0.59    34  0.57  molprobity  1.000  
44  44  0.95  Rotameric       11  62.830    25  0.57    39  0.67  molprobity  1.000  
45  45  0.88  Rotameric       11  59.890    25  0.42    39  0.79  molprobity  1.000  
46  46  0.88  Rotameric       12  51.930    25  0.56    37  0.51  molprobity  1.000  
47  47     ?  ?                ?  71.840     ?     ?     ?     ?  ?           0.840  
48  48     ?  ?                ?  60.800     ?     ?     ?     ?  ?           0.650  
49  49     ?  ?                ?  40.590     ?     ?     ?     ?  ?           0.450  
50  50     ?  ?                ?  57.360     ?     ?     ?     ?  ?           0.920  
51  51     ?  ?                ?  55.960     ?     ?     ?     ?  ?           0.580  
52  52     ?  ?                ?  62.160     ?     ?     ?     ?  ?           0.710  
53  53     ?  ?                ?  40.260     ?     ?     ?     ?  ?           0.870  
#
loop_
_pdbx_vrpt_instance_clashes.ordinal
_pdbx_vrpt_instance_clashes.instance_id
_pdbx_vrpt_instance_clashes.label_atom_id
_pdbx_vrpt_instance_clashes.cid
_pdbx_vrpt_instance_clashes.clashmag
_pdbx_vrpt_instance_clashes.dist
 1   6  "O2'"  1  0.68  1.93  
 2   6  "C2'"  2  0.58  2.33  
 3   7  "H5'"  1  0.68  1.93  
 4   7  "H5'"  2  0.58  2.33  
 5  12  "H2'"  3  0.47  2.47  
 6  13  C6     3  0.47  2.47  
 7  29  "O2'"  4  0.66  1.96  
 8  29  "C2'"  5  0.45  2.46  
 9  30  "H5'"  4  0.66  1.96  
10  30  "H5'"  5  0.45  2.46  
#
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  0.955  0.174  -0.096  
 2   2  20  0.963  0.126  -0.874  
 3   3  21  0.938  0.140       ?  
 4   4  23  0.957  0.135  -0.756  
 5   5  20  0.950  0.154  -0.450  
 6   6  20  0.952  0.117  -1.023  
 7   7  23  0.948  0.140  -0.660  
 8   8  22  0.912  0.150  -0.571  
 9   9  22  0.943  0.135  -0.849  
10  10  23  0.966  0.103  -1.366  
11  11  20  0.967  0.140  -0.641  
12  12  23  0.962  0.118  -1.080  
13  13  20  0.965  0.141  -0.680  
14  14  22  0.961  0.162  -0.348  
15  15  20  0.968  0.161  -0.326  
16  16  22  0.955  0.143  -0.701  
17  17  20  0.968  0.100  -1.405  
18  18  22  0.943  0.106  -1.388  
19  19  23  0.940  0.113  -1.176  
20  20  20  0.936  0.097  -1.458  
21  21  22  0.934  0.124  -1.054  
22  22  22  0.919  0.160  -0.385  
23  23  23  0.948  0.132  -0.813  
24  24  17  0.939  0.153  -0.467  
25  25  20  0.955  0.144  -0.575  
26  26  21  0.960  0.143       ?  
27  27  23  0.960  0.121  -1.023  
28  28  20  0.958  0.140  -0.697  
29  29  20  0.956  0.130  -0.807  
30  30  23  0.934  0.145  -0.565  
31  31  22  0.928  0.128  -0.980  
32  32  22  0.926  0.137  -0.812  
33  33  23  0.967  0.117  -1.099  
34  34  20  0.956  0.121  -0.957  
35  35  23  0.942  0.128  -0.889  
36  36  20  0.944  0.142  -0.662  
37  37  22  0.959  0.154  -0.496  
38  38  20  0.965  0.128  -0.910  
39  39  22  0.950  0.114  -1.240  
40  40  20  0.960  0.113  -1.175  
41  41  22  0.958  0.100  -1.500  
42  42  23  0.935  0.100  -1.424  
43  43  20  0.912  0.155  -0.432  
44  44  22  0.927  0.155  -0.478  
45  45  22  0.912  0.163  -0.329  
46  46  23  0.967  0.167  -0.145  
47  47   1  0.897  0.062       ?  
48  48   1  0.923  0.093       ?  
49  49   1  0.926  0.172       ?  
50  50   1  0.872  0.166       ?  
51  51   1  0.950  0.082       ?  
52  52   1  0.824  0.333       ?  
53  53   1  0.639  0.228       ?  
#
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        "1.8.5 (274361), CSD as541be (2020)"                                  Y  
3  eds          2.35                                                                  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  
##
