data_6U7Z

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  6U7Z
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    6U7Z
_pdbx_vrpt_summary.PDB_deposition_date         2019-09-03
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2023-10-11
_pdbx_vrpt_summary.RNA_suiteness               0.41
_pdbx_vrpt_summary.report_creation_date        2023-10-05:18:21
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,mogul,buster-report,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   Y
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "RNA (5'-R(*CP*UP*GP*CP*UP*GP*GP*CP*UP*AP*AP*GP*GP*GP*CP*CP*GP*AP*AP*AP*GP*(TG))-3')"  
2  polymer      "RNA (5'-R(*CP*UP*AP*UP*GP*CP*CP*UP*GP*CP*UP*G)-3')"  
3  non-polymer  "CYTIDINE-5'-MONOPHOSPHATE"  
4  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
D  4  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  2.71  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   70.02  141614     ?     ?  
2  2  1   83.75    3686  2.70  2.74  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    3276  2.70  2.74  
5  1  3   46.99  130704     ?     ?  
6  2  3   79.72    3359  2.70  2.74  
7  1  4   23.73    3102     ?     ?  
8  2  4   21.93    1067  2.44  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  2  B  100.00  
4  4  2  B  1  2  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  0.86  0.57  505  787  
2  1  2  B  B  0.89  0.45  275  426  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       3.60
_pdbx_vrpt_summary_geometry.num_H_reduce     371
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   780
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.53
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1213
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.87
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 400.000
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            59.785
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         84.305
_pdbx_vrpt_summary_diffraction.I_over_sigma              4.37(2.71A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3369
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.204
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.253
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.504
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.336
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.975
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-h-k,-l:0.060
_pdbx_vrpt_summary_diffraction.DCC_R                     0.17
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.24
_pdbx_vrpt_summary_diffraction.EDS_R                     0.18
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.71
_pdbx_vrpt_summary_diffraction.EDS_res_low               22.79
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[91.807,91.807,73.124,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.218
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 6.74% 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         96.31
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      162
_pdbx_vrpt_summary_diffraction.percent_free_reflections  4.81
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.71
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        45.59
_pdbx_vrpt_summary_diffraction.PDB_R                     0.17
_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_clashes
_pdbx_vrpt_model_instance.count_mogul_bond_outliers
_pdbx_vrpt_model_instance.count_mogul_angle_outliers
_pdbx_vrpt_model_instance.count_mogul_torsion_outliers
_pdbx_vrpt_model_instance.ligand_of_interest
 1  1  1  A   1  C    A    1  .  ?        2     ?     ?     ?  ?     
 2  1  1  A   2  U    A    2  .  ?        ?     ?     ?     ?  ?     
 3  1  1  A   3  G    A    3  .  ?        ?     ?     ?     ?  ?     
 4  1  1  A   4  C    A    4  .  ?        ?     ?     ?     ?  ?     
 5  1  1  A   5  U    A    5  .  ?        ?     ?     ?     ?  ?     
 6  1  1  A   6  G    A    6  .  ?        ?     ?     ?     ?  ?     
 7  1  1  A   7  G    A    7  .  ?        ?     ?     ?     ?  ?     
 8  1  1  A   8  C    A    8  .  ?        ?     ?     ?     ?  ?     
 9  1  1  A   9  U    A    9  .  ?        ?     ?     ?     ?  ?     
10  1  1  A  10  A    A   10  .  ?        ?     ?     ?     ?  ?     
11  1  1  A  11  A    A   11  .  ?        ?     ?     ?     ?  ?     
12  1  1  A  12  G    A   12  .  ?        1     ?     ?     ?  ?     
13  1  1  A  13  G    A   13  .  ?        1     ?     ?     ?  ?     
14  1  1  A  14  G    A   14  .  ?        ?     ?     ?     ?  ?     
15  1  1  A  15  C    A   15  .  ?        ?     ?     ?     ?  ?     
16  1  1  A  16  C    A   16  .  ?        ?     ?     ?     ?  ?     
17  1  1  A  17  G    A   17  .  ?        ?     ?     ?     ?  ?     
18  1  1  A  18  A    A   18  .  ?        1     ?     ?     ?  ?     
19  1  1  A  19  A    A   19  .  ?        1     ?     ?     ?  ?     
20  1  1  A  20  A    A   20  .  ?        ?     ?     ?     ?  ?     
21  1  1  A  21  G    A   21  .  ?        ?     ?     ?     ?  ?     
22  1  1  A  22  TG   A   22  .  ?        ?     3     5     1  Y     
23  1  2  B   1  C    B    1  .  ?        ?     ?     ?     ?  ?     
24  1  2  B   2  U    B    2  .  ?        ?     ?     ?     ?  ?     
25  1  2  B   3  A    B    3  .  ?        1     ?     ?     ?  ?     
26  1  2  B   4  U    B    4  .  ?        1     ?     ?     ?  ?     
27  1  2  B   5  G    B    5  .  ?        ?     ?     ?     ?  ?     
28  1  2  B   6  C    B    6  .  ?        ?     ?     ?     ?  ?     
29  1  2  B   7  C    B    7  .  ?        ?     ?     ?     ?  ?     
30  1  2  B   8  U    B    8  .  ?        ?     ?     ?     ?  ?     
31  1  2  B   9  G    B    9  .  ?        ?     ?     ?     ?  ?     
32  1  2  B  10  C    B   10  .  ?        ?     ?     ?     ?  ?     
33  1  2  B  11  U    B   11  .  ?        ?     ?     ?     ?  ?     
34  1  2  B  12  G    B   12  .  ?        ?     ?     ?     ?  ?     
35  1  3  C   .  C    A  101  .  ?        ?     ?     1     3  ?     
36  1  4  D   .  HOH  A  201  .  ?        ?     ?     ?     ?  ?     
#
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.RNA_pucker
_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   94.230    19  0.64    30  0.62  molprobity  1.000  
 2   2  0.56  Rotameric          ?          10  101.840    22  0.53    34  0.65  molprobity  1.000  
 3   3  0.29  Rotameric          ?          11  107.620    26  0.31    41  0.80  molprobity  1.000  
 4   4  0.43  Rotameric          ?          11  117.860    22  0.49    34  0.83  molprobity  1.000  
 5   5  0.48  Rotameric          ?          10  115.720    22  0.59    34  0.96  molprobity  1.000  
 6   6  0.47  Rotameric          ?          11   98.750    26  0.32    41  0.82  molprobity  1.000  
 7   7  0.84  Rotameric          ?          11   95.170    26  0.50    41  0.79  molprobity  1.000  
 8   8  0.39  Rotameric          ?          11   79.410    22  0.53    34  0.89  molprobity  1.000  
 9   9  0.78  Rotameric          ?          10   77.200    22  0.32    34  0.63  molprobity  1.000  
10  10  0.00  Triaged/NotBinned  outlier    11   78.300    25  0.68    39  1.02  molprobity  1.000  
11  11  0.00  Triaged/NotBinned  ?          11   85.760    25  0.60    39  1.06  molprobity  1.000  
12  12  0.01  Rotameric          ?          11   86.080    26  0.41    41  0.92  molprobity  1.000  
13  13  0.42  Rotameric          ?          11   89.600    26  0.96    41  0.83  molprobity  1.000  
14  14  0.04  Rotameric          ?          11   90.390    26  0.93    41  0.93  molprobity  1.000  
15  15  0.07  Rotameric          ?          11   98.510    22  0.64    34  0.88  molprobity  1.000  
16  16  0.13  Rotameric          ?          11   93.250    22  0.45    34  0.98  molprobity  1.000  
17  17  0.72  Rotameric          ?          11   94.450    26  0.28    41  0.68  molprobity  1.000  
18  18  0.69  Rotameric          ?          11   83.680    25  0.54    39  0.88  molprobity  1.000  
19  19  0.18  Rotameric          ?          11   75.950    25  0.45    39  1.06  molprobity  1.000  
20  20  0.52  Rotameric          ?          11   81.040    25  0.65    39  0.79  molprobity  1.000  
21  21  0.24  Rotameric          ?          11   84.780    25  0.51    37  0.88  molprobity  1.000  
22  22     ?  ?                  ?           ?   89.450    16  1.95    16  1.96  mogul       1.000  
23  23  0.00  NotAvailable       ?          12   91.210    19  0.43    30  0.86  molprobity  1.000  
24  24  0.29  Rotameric          ?          10   87.810    22  0.63    34  0.96  molprobity  1.000  
25  25  0.00  NonRotameric       ?          11   85.720    25  0.38    39  1.21  molprobity  1.000  
26  26  0.00  NonRotameric       ?          10   85.660    22  0.32    34  0.73  molprobity  1.000  
27  27  0.00  Triaged/NotBinned  ?          11   81.510    26  0.44    41  0.59  molprobity  1.000  
28  28  0.65  Rotameric          ?          11   74.210    22  0.76    34  1.29  molprobity  1.000  
29  29  0.84  Rotameric          ?          11   78.500    22  0.37    34  0.82  molprobity  1.000  
30  30  0.00  Triaged/NotBinned  ?          10  100.320    22  0.49    34  0.77  molprobity  1.000  
31  31  0.00  Triaged/NotBinned  ?          11  103.800    26  0.30    41  1.08  molprobity  1.000  
32  32  0.29  Rotameric          ?          11  113.710    22  0.37    34  0.72  molprobity  1.000  
33  33  0.80  Rotameric          ?          10  114.480    22  0.35    34  0.71  molprobity  1.000  
34  34  0.42  Rotameric          ?          12  118.110    25  0.40    37  0.60  molprobity  1.000  
35  35  0.00  NotAvailable       ?          12  114.420    22  0.48    33  0.67  mogul       1.000  
36  36     ?  ?                  ?           ?   94.960     ?     ?     ?     ?  ?           1.000  
#
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   1  O2     1  0.47  2.14  
2   1  "H2'"  1  0.47  2.14  
3  12  "H2'"  2  0.45  2.17  
4  13  "O4'"  2  0.45  2.17  
5  18  "H2'"  3  0.50  2.46  
6  19  C8     3  0.50  2.46  
7  25  "H1'"  4  0.42  2.54  
8  26  C5     4  0.42  2.54  
#
loop_
_pdbx_vrpt_instance_mogul_bond_outliers.ordinal
_pdbx_vrpt_instance_mogul_bond_outliers.instance_id
_pdbx_vrpt_instance_mogul_bond_outliers.atom_1
_pdbx_vrpt_instance_mogul_bond_outliers.atom_2
_pdbx_vrpt_instance_mogul_bond_outliers.obsval
_pdbx_vrpt_instance_mogul_bond_outliers.mean
_pdbx_vrpt_instance_mogul_bond_outliers.numobs
_pdbx_vrpt_instance_mogul_bond_outliers.stdev
_pdbx_vrpt_instance_mogul_bond_outliers.Zscore
_pdbx_vrpt_instance_mogul_bond_outliers.mindiff
1  22  "O4'"  "C1'"  1.47  1.41  123  0.01   3.86  0.02  
2  22  C5     C4     1.36  1.43   44  0.03  -2.72  0.01  
3  22  C5     C6     1.36  1.47   49  0.02  -5.33  0.04  
#
loop_
_pdbx_vrpt_instance_mogul_angle_outliers.ordinal
_pdbx_vrpt_instance_mogul_angle_outliers.instance_id
_pdbx_vrpt_instance_mogul_angle_outliers.atom_1
_pdbx_vrpt_instance_mogul_angle_outliers.atom_2
_pdbx_vrpt_instance_mogul_angle_outliers.atom_3
_pdbx_vrpt_instance_mogul_angle_outliers.obsval
_pdbx_vrpt_instance_mogul_angle_outliers.mean
_pdbx_vrpt_instance_mogul_angle_outliers.numobs
_pdbx_vrpt_instance_mogul_angle_outliers.stdev
_pdbx_vrpt_instance_mogul_angle_outliers.Zscore
_pdbx_vrpt_instance_mogul_angle_outliers.mindiff
1  22  "C3'"  "C2'"  "C1'"  105.99   99.92  270  2.22   2.74  0.03  
2  22  C5     C6     N1     118.89  113.95   45  1.77   2.80  2.05  
3  22  O6     C6     N1     116.59  120.65  314  1.18  -3.43  0.13  
4  22  C2     N1     C6     117.85  125.10  790  1.84  -3.94  0.27  
5  22  C8     N7     C5     108.40  102.99   26  1.90   2.84  1.36  
6  35  OP2    P      OP1    119.07  110.68  447  3.91   2.14  0.23  
#
loop_
_pdbx_vrpt_instance_mogul_torsion_outliers.ordinal
_pdbx_vrpt_instance_mogul_torsion_outliers.instance_id
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_1
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_2
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_3
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_4
_pdbx_vrpt_instance_mogul_torsion_outliers.obsval
_pdbx_vrpt_instance_mogul_torsion_outliers.mean
_pdbx_vrpt_instance_mogul_torsion_outliers.numobs
_pdbx_vrpt_instance_mogul_torsion_outliers.stdev
_pdbx_vrpt_instance_mogul_torsion_outliers.mindiff
_pdbx_vrpt_instance_mogul_torsion_outliers.local_density
1  22  "C2'"  "C3'"  "O3'"  P       177.41  49.55   49  26.57  3.17  4.08  
2  35  "C4'"  "C5'"  "O5'"  P      -105.45  51.47  432  17.28  1.83  1.85  
3  35  "O4'"  "C4'"  "C5'"  "O5'"   -92.39  29.51  451  13.54  0.02  1.11  
4  35  "C3'"  "C4'"  "C5'"  "O5'"    27.57  42.23  451  40.86  0.93  2.22  
#
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  0.974  0.171  -0.149  
 2   2  20  0.955  0.122  -0.940  
 3   3  23  0.948  0.109  -1.252  
 4   4  20  0.955  0.154  -0.450  
 5   5  20  0.941  0.090  -1.472  
 6   6  23  0.965  0.081  -1.786  
 7   7  23  0.971  0.108  -1.271  
 8   8  20  0.978  0.116  -1.122  
 9   9  20  0.972  0.133  -0.757  
10  10  22  0.960  0.144  -0.682  
11  11  22  0.965  0.152  -0.533  
12  12  23  0.971  0.124  -0.966  
13  13  23  0.948  0.126  -0.927  
14  14  23  0.941  0.105  -1.328  
15  15  20  0.948  0.122  -1.016  
16  16  20  0.965  0.107  -1.281  
17  17  23  0.981  0.098  -1.462  
18  18  22  0.984  0.137  -0.812  
19  19  22  0.977  0.121  -1.110  
20  20  22  0.961  0.122  -1.091  
21  21  23  0.971  0.127  -0.908  
22  22  21  0.950  0.128       ?  
23  23  17  0.959  0.145  -0.609  
24  24  20  0.966  0.113  -1.090  
25  25  22  0.972  0.183   0.043  
26  26  20  0.965  0.167  -0.193  
27  27  23  0.968  0.190   0.294  
28  28  20  0.970  0.166  -0.237  
29  29  20  0.972  0.125  -0.963  
30  30  20  0.956  0.097  -1.355  
31  31  23  0.949  0.090  -1.615  
32  32  20  0.952  0.122  -1.016  
33  33  20  0.929  0.118  -1.007  
34  34  23  0.948  0.147  -0.527  
35  35  21  0.943  0.133       ?  
36  36   1  0.912  0.121       ?  
#
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          2.35.1                                                                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  
##
