data_7E9I

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7E9I
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7E9I
_pdbx_vrpt_summary.PDB_deposition_date         2021-03-04
_pdbx_vrpt_summary.PDB_revision_number         2
_pdbx_vrpt_summary.PDB_revision_date           2023-11-29
_pdbx_vrpt_summary.RNA_suiteness               0.58
_pdbx_vrpt_summary.report_creation_date        2023-11-20:16:18
_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      "33-mer RNA"  
2  non-polymer  2-azanyl-5-[[2-(3-but-3-ynyl-1,2-diazirin-3-yl)ethylamino]methyl]-1,7-dihydropyrrolo[2,3-d]pyrimidin-4-one  
3  non-polymer  "SULFATE ION"  
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  2.8  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  38.61  141614     ?     ?  
2  2  1  66.27    3569  2.80  2.80  
3  1  2  49.84  127900     ?     ?  
4  2  2  39.96    3078  2.80  2.80  
5  1  3  46.99  130704     ?     ?  
6  2  3  82.22    3140  2.80  2.80  
7  1  4  59.28    3102     ?     ?  
8  2  4  65.85    1227  2.50  3.10  
#
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  49.84  
2  4  2  A  1  1  A  39.96  
#
_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      1.18
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.64
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   767
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  1192
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       7.53
_pdbx_vrpt_summary_geometry.num_H_reduce     350
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   767
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.64
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1192
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.18
#
_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            21.617
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         72.004
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.67(2.81A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        5794
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.460
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.173
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.493
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.326
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.965
_pdbx_vrpt_summary_diffraction.DCC_R                     0.19
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.24
_pdbx_vrpt_summary_diffraction.EDS_R                     0.20
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.80
_pdbx_vrpt_summary_diffraction.EDS_res_low               41.02
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[88.904,88.904,47.122,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.557
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 5.84% 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         2
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         98.04
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      290
_pdbx_vrpt_summary_diffraction.percent_free_reflections  5.01
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     3.03
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.80
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        41.00
_pdbx_vrpt_summary_diffraction.PDB_R                     0.20
_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_angle_outliers
_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
 1  1  1  A   1  C    A    1  .  ?        ?     ?     ?     ?     ?  
 2  1  1  A   2  U    A    2  .  ?        ?     ?     ?     ?     ?  
 3  1  1  A   3  G    A    3  .  ?        1     ?     ?     ?     ?  
 4  1  1  A   4  G    A    4  .  ?        ?     ?     ?     ?     ?  
 5  1  1  A   5  G    A    5  .  ?        ?     ?     ?     ?     ?  
 6  1  1  A   6  U    A    6  .  ?        ?     ?     ?     ?     ?  
 7  1  1  A   7  C    A    7  .  ?        ?     ?     ?     ?     ?  
 8  1  1  A   8  G    A    8  .  ?        ?     ?     ?     ?     ?  
 9  1  1  A   9  C    A    9  .  ?        ?     1     ?     ?     ?  
10  1  1  A  10  A    A   10  .  ?        ?     2     ?     ?     ?  
11  1  1  A  11  G    A   11  .  ?        ?     ?     ?     ?     ?  
12  1  1  A  12  U    A   12  .  ?        ?     ?     ?     ?     ?  
13  1  1  A  13  A    A   13  .  ?        1     3     ?     ?     ?  
14  1  1  A  14  A    A   14  .  ?        ?     3     ?     ?     ?  
15  1  1  A  15  C    A   15  .  ?        ?     ?     ?     ?     ?  
16  1  1  A  16  C    A   16  .  ?        ?     ?     ?     ?     ?  
17  1  1  A  17  C    A   17  .  ?        ?     ?     ?     ?     ?  
18  1  1  A  18  C    A   18  .  ?        ?     ?     ?     ?     ?  
19  1  1  A  19  A    A   19  .  ?        ?     1     ?     ?     ?  
20  1  1  A  20  G    A   20  .  ?        ?     1     ?     ?     ?  
21  1  1  A  21  U    A   21  .  ?        ?     ?     ?     ?     ?  
22  1  1  A  22  U    A   22  .  ?        ?     1     ?     ?     ?  
23  1  1  A  23  A    A   23  .  ?        ?     ?     ?     ?     ?  
24  1  1  A  24  A    A   24  .  ?        ?     ?     ?     ?     ?  
25  1  1  A  25  C    A   25  .  ?        ?     ?     ?     ?     ?  
26  1  1  A  26  A    A   26  .  ?        ?     ?     ?     ?     ?  
27  1  1  A  27  A    A   27  .  ?        ?     1     ?     ?     ?  
28  1  1  A  28  A    A   28  .  ?        ?     1     ?     ?     ?  
29  1  1  A  29  A    A   29  .  ?        ?     ?     ?     ?     ?  
30  1  1  A  30  C    A   30  .  ?        ?     ?     ?     ?     ?  
31  1  1  A  31  A    A   31  .  ?        ?     1     ?     ?     ?  
32  1  1  A  32  A    A   32  .  ?        ?     ?     ?     ?     ?  
33  1  1  A  33  G    A   33  .  ?        ?     ?     ?     ?     ?  
34  1  2  B   .  J0C  A  101  .  ?        ?     ?     8     3     2  
35  1  3  C   .  SO4  A  102  .  ?        ?     ?     ?     ?     ?  
36  1  4  D   .  HOH  A  201  .  ?        ?     1     ?     ?     ?  
37  1  4  D   .  HOH  A  202  .  ?        ?     ?     ?     ?     ?  
#
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   71.390    19  1.16    30  1.90  molprobity  1.000  
 2   2  0.84  Rotameric            10   70.700    22  0.75    34  1.30  molprobity  1.000  
 3   3  0.79  Rotameric            11   64.440    26  0.88    41  2.06  molprobity  1.000  
 4   4  0.83  Rotameric            11   75.010    26  0.59    41  1.00  molprobity  1.000  
 5   5  0.93  Rotameric            11   76.610    26  0.46    41  1.19  molprobity  1.000  
 6   6  0.29  Rotameric            10   78.730    22  0.50    34  0.89  molprobity  1.000  
 7   7  0.60  Rotameric            11   85.610    22  0.62    34  0.92  molprobity  1.000  
 8   8  0.32  Rotameric            11   93.240    26  0.35    41  0.99  molprobity  1.000  
 9   9  0.77  Rotameric            11   96.770    22  0.46    34  0.71  molprobity  1.000  
10  10  0.48  Rotameric            11   97.960    25  0.42    39  1.01  molprobity  1.000  
11  11  0.60  Rotameric            11   91.670    26  0.67    41  1.43  molprobity  1.000  
12  12     ?  ?                     ?  110.000     3  0.61     3  2.03  molprobity  1.000  
13  13  0.00  NotAvailable         11  175.990    25  1.07    39  1.69  molprobity  0.930  
14  14  0.04  Rotameric            11  123.770    25  0.85    39  1.28  molprobity  1.000  
15  15  0.58  Rotameric            11   99.900    22  0.57    34  1.07  molprobity  1.000  
16  16  0.90  Rotameric            11   80.430    22  0.62    34  1.02  molprobity  1.000  
17  17  0.89  Rotameric            11   73.510    22  0.74    34  0.92  molprobity  1.000  
18  18  0.96  Rotameric            11   69.570    22  0.70    34  1.48  molprobity  1.000  
19  19  0.50  Rotameric            11   65.090    25  0.81    39  1.21  molprobity  1.000  
20  20  0.41  Rotameric            11   63.180    26  0.79    41  1.27  molprobity  1.000  
21  21  0.35  Rotameric            10   75.690    22  0.46    34  1.05  molprobity  1.000  
22  22  0.61  Rotameric            10   67.410    22  0.60    34  1.14  molprobity  1.000  
23  23  0.53  Rotameric            11   68.130    25  0.44    39  0.86  molprobity  1.000  
24  24  0.20  Rotameric            11   73.070    25  0.57    39  1.16  molprobity  1.000  
25  25  0.40  Rotameric            11   77.920    22  0.59    34  1.02  molprobity  1.000  
26  26  0.00  Triaged/NotBinned    11   81.030    25  0.47    39  0.89  molprobity  1.000  
27  27  0.56  Rotameric            11   84.250    25  0.55    39  0.97  molprobity  1.000  
28  28  0.40  Rotameric            11   91.180    25  0.46    39  0.89  molprobity  1.000  
29  29  0.00  Triaged/NotBinned    11   90.590    25  0.58    39  1.26  molprobity  1.000  
30  30  0.52  Rotameric            11   93.520    22  0.54    34  0.76  molprobity  1.000  
31  31  0.82  Rotameric            11   97.450    25  0.57    39  0.80  molprobity  1.000  
32  32  0.00  Triaged/NotBinned    11  119.450    25  0.47    39  0.73  molprobity  1.000  
33  33  0.00  Triaged/NotBinned    12  101.360    25  0.53    37  1.40  molprobity  1.000  
34  34     ?  ?                     ?   97.740    18  3.17    14  2.06  mogul       1.000  
35  35     ?  ?                     ?  147.020     4  0.15     6  0.22  mogul       0.530  
36  36     ?  ?                     ?   67.110     ?     ?     ?     ?  ?           0.790  
37  37     ?  ?                     ?   55.030     ?     ?     ?     ?  ?           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   9  "H2'"  1  0.40  2.21  
 2  10  C6     2  0.49  3.00  
 3  10  "O4'"  1  0.40  2.21  
 4  13  "H2'"  3  0.61  2.36  
 5  13  "H2'"  4  0.51  1.74  
 6  13  "H2'"  5  0.48  2.13  
 7  14  C8     3  0.61  2.36  
 8  14  H8     4  0.51  1.74  
 9  14  "O4'"  5  0.48  2.13  
10  19  "O2'"  6  0.43  2.19  
11  20  "H5'"  6  0.43  2.19  
12  22  "H1'"  7  0.44  2.18  
13  27  "O2'"  8  0.44  2.17  
14  28  "H5'"  8  0.44  2.17  
15  31  C6     2  0.49  3.00  
16  36  O      7  0.44  2.18  
#
loop_
_pdbx_vrpt_instance_intra_angle_outliers.ordinal
_pdbx_vrpt_instance_intra_angle_outliers.instance_id
_pdbx_vrpt_instance_intra_angle_outliers.atom_1
_pdbx_vrpt_instance_intra_angle_outliers.atom_2
_pdbx_vrpt_instance_intra_angle_outliers.atom_3
_pdbx_vrpt_instance_intra_angle_outliers.obs
_pdbx_vrpt_instance_intra_angle_outliers.mean
_pdbx_vrpt_instance_intra_angle_outliers.stdev
_pdbx_vrpt_instance_intra_angle_outliers.Z
1   3  N1  C6  O6  115.889  119.900  0.600  -6.69  
2  13  C8  N9  C4  103.778  105.800  0.400  -5.06  
#
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  34  C8   C2   1.52  1.47    49  0.01   3.94  0.03  
2  34  C2   N3   1.43  1.39    44  0.02   2.37  0.02  
3  34  O1   C2   1.19  1.23   534  0.02  -2.60  0.00  
4  34  C4   N3   1.45  1.33  1024  0.02   4.98  0.00  
5  34  C4   N5   1.46  1.34  1382  0.02   5.13  0.00  
6  34  C4   N6   1.46  1.37  1013  0.02   3.45  0.00  
7  34  C7   N6   1.48  1.38    97  0.01   8.48  0.08  
8  34  C18  C19  1.54  1.47   204  0.02   3.29  0.00  
#
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  34  N6   C7  N22  130.46  123.18  21  1.15   6.31  4.22  
2  34  C10  C9  C21  124.38  127.67  36  1.41  -2.34  0.11  
3  34  C7   N6  C4   118.68  122.92  31  1.99  -2.13  0.95  
#
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  34  C14  C17  C18  C19   116.80  53.16   44   9.37  17.42  0.00  
2  34  C13  C12  N11  C10  -142.07  35.44  500  14.60   0.11  1.20  
#
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  0.965  0.192   0.326  
 2   2  20  0.946  0.184   0.153  
 3   3  23  0.961  0.163   0.020  
 4   4  23  0.974  0.155  -0.103  
 5   5  23  0.976  0.166   0.066  
 6   6  20  0.968  0.153  -0.236  
 7   7  20  0.977  0.194   0.354  
 8   8  23  0.972  0.127  -0.534  
 9   9  20  0.969  0.149  -0.266  
10  10  22  0.964  0.158  -0.174  
11  11  23  0.970  0.185   0.358  
12  12   4  0.949  0.224   0.654  
13  13  22  0.581  0.377   3.028  
14  14  22  0.893  0.203   0.484  
15  15  20  0.948  0.180   0.161  
16  16  20  0.952  0.184   0.216  
17  17  20  0.961  0.179   0.147  
18  18  20  0.976  0.150  -0.252  
19  19  22  0.977  0.171   0.016  
20  20  23  0.973  0.183   0.328  
21  21  20  0.979  0.174   0.028  
22  22  20  0.976  0.175   0.040  
23  23  22  0.970  0.175   0.075  
24  24  22  0.980  0.163  -0.101  
25  25  20  0.978  0.140  -0.390  
26  26  22  0.964  0.143  -0.393  
27  27  22  0.973  0.142  -0.408  
28  28  22  0.964  0.153  -0.247  
29  29  22  0.971  0.154  -0.232  
30  30  20  0.974  0.144  -0.335  
31  31  22  0.969  0.172   0.031  
32  32  22  0.970  0.160  -0.145  
33  33  23  0.960  0.149  -0.195  
34  34  22  0.904  0.327       ?  
35  35   5  0.939  0.207       ?  
36  36   1  0.911  0.345       ?  
37  37   1  0.904  0.266       ?  
#
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          2.36                                                                  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  
##
