data_9DYW

_audit_conform.dict_name      mmcif_pdbx_vrpt.dic
_audit_conform.dict_version   0.068
_audit_conform.dict_location  https://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx_vrpt.dic
#
_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  9DYW
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    9DYW
_pdbx_vrpt_summary.PDB_deposition_date         2024-10-15
_pdbx_vrpt_summary.PDB_revision_number         1
_pdbx_vrpt_summary.PDB_revision_date           2025-03-26
_pdbx_vrpt_summary.report_creation_date        2025-03-16:18:06
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds_mogul,validation_schema,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  VVGGVV  
2  water    water   
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  2  
D  2  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  1.1  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore           
2  Ramachandran_outlier_percent  
3  rotamer_outliers_percent      
4  RSRZ_outliers_percent         
5  R_value_R_free                
#
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  180529     ?     ?  
 2  2  1  100.00    1561  1.08  1.12  
 3  1  2  100.00  177936     ?     ?  
 4  2  2  100.00    1524  1.08  1.12  
 5  1  3  100.00  177891     ?     ?  
 6  2  3  100.00    1520  1.08  1.12  
 7  1  4  100.00  164620     ?     ?  
 8  2  4  100.00    1365  1.08  1.12  
 9  1  5   95.97  164625     ?     ?  
10  2  5   44.63    1365  1.08  1.12  
#
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  5  3  A  1  1  A  100.00  
 4  6  3  A  1  1  A  100.00  
 5  7  4  A  1  1  A  100.00  
 6  8  4  A  1  1  A  100.00  
 7  3  2  B  1  1  B  100.00  
 8  4  2  B  1  1  B  100.00  
 9  5  3  B  1  1  B  100.00  
10  6  3  B  1  1  B  100.00  
11  7  4  B  1  1  B  100.00  
12  8  4  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  0.84  0.62  43  57  
2  1  1  B  B  0.83  0.54  36  47  
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       0.00
_pdbx_vrpt_summary_geometry.clashscore                     0.00
_pdbx_vrpt_summary_geometry.num_H_reduce                   97
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 79
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.59
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                104
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.84
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            83.520
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.273
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.975
_pdbx_vrpt_summary_diffraction.DCC_R                     0.1516
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.1686
_pdbx_vrpt_summary_diffraction.EDS_R                     0.1556
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.10
_pdbx_vrpt_summary_diffraction.EDS_res_low               15.03
_pdbx_vrpt_summary_diffraction.B_factor_type             FULL
_pdbx_vrpt_summary_diffraction.data_completeness         89.42
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      462
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.01
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.10
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        15.03
_pdbx_vrpt_summary_diffraction.PDB_R                     0.1520
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.1672
_pdbx_vrpt_summary_diffraction.density_fitness_version   1.0.11
_pdbx_vrpt_summary_diffraction.CCP4_version              "9.0.004 (Gargrove)"
#
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
 1  1  1  A  1  VAL  A    1  .  ?     
 2  1  1  A  2  VAL  A    2  A  ?     
 3  1  1  A  2  VAL  A    2  B  ?     
 4  1  1  A  3  GLY  A    3  .  ?     
 5  1  1  A  4  GLY  A    4  .  ?     
 6  1  1  A  5  VAL  A    5  .  ?     
 7  1  1  A  6  VAL  A    6  .  ?     
 8  1  1  B  1  VAL  B    1  .  ?     
 9  1  1  B  2  VAL  B    2  .  ?     
10  1  1  B  3  GLY  B    3  .  ?     
11  1  1  B  4  GLY  B    4  .  ?     
12  1  1  B  5  VAL  B    5  .  ?     
13  1  1  B  6  VAL  B    6  .  ?     
14  1  2  C  .  HOH  A  101  .  ?     
15  1  2  C  .  HOH  A  102  A  ?     
16  1  2  C  .  HOH  A  102  B  ?     
17  1  2  C  .  HOH  A  102  C  ?     
18  1  2  C  .  HOH  A  103  .  ?     
19  1  2  D  .  HOH  B  101  .  ?     
20  1  2  D  .  HOH  B  102  .  ?     
21  1  2  D  .  HOH  B  103  A  ?     
22  1  2  D  .  HOH  B  104  B  ?     
23  1  2  D  .  HOH  B  105  .  ?     
24  1  2  D  .  HOH  B  106  .  ?     
25  1  2  D  .  HOH  B  107  .  ?     
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.rotamer_class
_pdbx_vrpt_model_instance_geometry.phi
_pdbx_vrpt_model_instance_geometry.psi
_pdbx_vrpt_model_instance_geometry.ramachandran_class
_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  m          ?       ?  ?          11   5.980     7  0.74    10  0.75  molprobity  1.000  
 2   2  p     -137.4   147.4  Favored     9   3.980     7  0.58    10  1.06  molprobity  0.640  
 3   3  p     -137.4   147.4  Favored     9   3.980     7  0.58    10  1.06  molprobity  0.640  
 4   4  ?      -74.9   155.4  Favored     3   6.720     4  0.40     5  0.52  molprobity  1.000  
 5   5  ?      -80.4  -169.8  Favored     3   6.240     4  0.47     5  0.73  molprobity  1.000  
 6   6  m     -133.2   150.6  Favored     9   6.250     7  0.46    10  0.71  molprobity  1.000  
 7   7  m          ?       ?  ?           9   8.360     7  0.87     7  0.66  molprobity  1.000  
 8   8  m          ?       ?  ?          11   7.090     7  0.50    10  0.84  molprobity  1.000  
 9   9  t     -104.5   122.4  Favored     9   6.190     7  0.49    10  0.70  molprobity  1.000  
10  10  ?      -78.2   171.8  Favored     3   5.370     4  0.32     5  0.57  molprobity  1.000  
11  11  ?      -77.5   161.9  Favored     3   5.190     4  0.34     5  1.05  molprobity  1.000  
12  12  m     -128.1   155.2  Favored     9   6.330     7  0.62    10  0.71  molprobity  1.000  
13  13  m          ?       ?  ?           9   7.040     7  0.72     7  1.09  molprobity  1.000  
14  14  ?          ?       ?  ?           ?  11.960     ?     ?     ?     ?  ?           1.000  
15  15  ?          ?       ?  ?           ?   2.590     ?     ?     ?     ?  ?           0.330  
16  16  ?          ?       ?  ?           ?   2.590     ?     ?     ?     ?  ?           0.330  
17  17  ?          ?       ?  ?           ?   2.590     ?     ?     ?     ?  ?           0.330  
18  18  ?          ?       ?  ?           ?   6.560     ?     ?     ?     ?  ?           0.500  
19  19  ?          ?       ?  ?           ?  12.800     ?     ?     ?     ?  ?           1.000  
20  20  ?          ?       ?  ?           ?   9.710     ?     ?     ?     ?  ?           1.000  
21  21  ?          ?       ?  ?           ?   5.880     ?     ?     ?     ?  ?           0.500  
22  22  ?          ?       ?  ?           ?   7.570     ?     ?     ?     ?  ?           0.500  
23  23  ?          ?       ?  ?           ?   9.190     ?     ?     ?     ?  ?           1.000  
24  24  ?          ?       ?  ?           ?   8.500     ?     ?     ?     ?  ?           1.000  
25  25  ?          ?       ?  ?           ?   7.220     ?     ?     ?     ?  ?           1.000  
#
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
_pdbx_vrpt_model_instance_density.EDIAm
_pdbx_vrpt_model_instance_density.OPIA
 1   1  18  0.981  0.037  -0.556  0.889   85.710  
 2   2  28  0.984  0.045  -0.197  0.764   61.900  
 3   3  28  0.984  0.045  -0.197  0.764   61.900  
 4   4   7  0.978  0.036  -0.426  0.872  100.000  
 5   5   7  0.986  0.030  -0.623  0.915  100.000  
 6   6  16  0.978  0.043  -0.287  0.852   57.140  
 7   7  17  0.951  0.070   0.924  0.797   57.140  
 8   8  18  0.983  0.034  -0.691  0.878   85.710  
 9   9  16  0.982  0.039  -0.466  0.897   85.710  
10  10   7  0.993  0.022  -0.885  0.911  100.000  
11  11   7  0.991  0.035  -0.459  0.956  100.000  
12  12  16  0.986  0.032  -0.780  0.862   71.430  
13  13  17  0.974  0.049  -0.018  0.850   57.140  
14  14   1  0.987  0.034       ?  0.886  100.000  
15  15   3  0.812  0.334       ?  0.603    0.000  
16  16   3  0.812  0.334       ?  0.603    0.000  
17  17   3  0.812  0.334       ?  0.603    0.000  
18  18   1  0.722  0.383       ?  0.000    0.000  
19  19   1  0.986  0.086       ?  0.944  100.000  
20  20   1  0.993  0.025       ?  0.952  100.000  
21  21   1  0.969  0.154       ?  0.749    0.000  
22  22   1  0.975  0.139       ?  0.401    0.000  
23  23   1  0.990  0.043       ?  0.961  100.000  
24  24   1  0.991  0.024       ?  0.952  100.000  
25  25   1  0.994  0.047       ?  1.016  100.000  
#
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  eds          3.0                                                                   Y  
3  dcc          '"2.29  (2024-07-11))"'                                               Y  
4  xtriage      1.21                                                                  N  
5  percentiles  "20231227.v01 (using entries in the PDB archive December 27th 2023)"  Y  
##
