data_8QWV

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  8QWV
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    8QWV
_pdbx_vrpt_summary.PDB_deposition_date         2023-10-20
_pdbx_vrpt_summary.PDB_revision_number         1
_pdbx_vrpt_summary.PDB_revision_date           2024-08-07
_pdbx_vrpt_summary.report_creation_date        2024-07-29:12:31
_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      "Peptide LYIQNL"  
2  non-polymer  ETHANOL  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  2  
D  2  
E  3  
F  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  1.7  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   40.89  141614     ?     ?  
 2  2  1   27.18    4695  1.70  1.70  
 3  1  2  100.00  138981     ?     ?  
 4  2  2  100.00    4610  1.70  1.70  
 5  1  3  100.00  138945     ?     ?  
 6  2  3  100.00    4610  1.70  1.70  
 7  1  4   10.97  127900     ?     ?  
 8  2  4   12.70    4222  1.70  1.70  
 9  1  5   89.99  130704     ?     ?  
10  2  5   89.33    4298  1.70  1.70  
#
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    1.22  
 6  8  4  A  1  1  A    1.33  
 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  0.55  0.34  75  97  
2  1  1  B  B  0.51  0.33  54  71  
#
_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                     7.09
_pdbx_vrpt_summary_geometry.num_H_reduce                   152
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 129
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.34
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                168
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.53
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 10.000
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            413.711
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         8.595
_pdbx_vrpt_summary_diffraction.I_over_sigma              3.26(1.69A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        988
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.100
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            1.154
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.486
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.321
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.961
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-k,-h-l:0.290
_pdbx_vrpt_summary_diffraction.DCC_R                     0.16
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.19
_pdbx_vrpt_summary_diffraction.EDS_R                     0.18
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.70
_pdbx_vrpt_summary_diffraction.EDS_res_low               19.66
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[10.983,5.557,10.716,0.000,-1.097,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.597
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 39.36 % 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 3.2126e-04. 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         3
_pdbx_vrpt_summary_diffraction.centric_outliers          1
_pdbx_vrpt_summary_diffraction.data_completeness         89.74
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      103
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.43
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     8.33
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.70
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        19.66
_pdbx_vrpt_summary_diffraction.PDB_R                     0.16
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.19
#
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  LEU  A    1  .  ?        1  
 2  1  1  A  2  TYR  A    2  A  ?        ?  
 3  1  1  A  2  TYR  A    2  B  ?        ?  
 4  1  1  A  3  ILE  A    3  .  ?        1  
 5  1  1  A  4  GLN  A    4  .  ?        ?  
 6  1  1  A  5  ASN  A    5  .  ?        ?  
 7  1  1  A  6  LEU  A    6  A  ?        ?  
 8  1  1  A  6  LEU  A    6  B  ?        ?  
 9  1  1  B  1  LEU  B    1  .  ?        1  
10  1  1  B  2  TYR  B    2  .  ?        ?  
11  1  1  B  3  ILE  B    3  .  ?        ?  
12  1  1  B  4  GLN  B    4  .  ?        ?  
13  1  1  B  5  ASN  B    5  .  ?        ?  
14  1  1  B  6  LEU  B    6  .  ?        ?  
15  1  2  C  .  EOH  B  101  A  ?        ?  
16  1  2  C  .  EOH  B  101  B  ?        ?  
17  1  2  D  .  EOH  B  102  .  ?        ?  
18  1  3  E  .  HOH  A  101  .  ?        ?  
19  1  3  E  .  HOH  A  102  .  ?        ?  
20  1  3  E  .  HOH  A  103  .  ?        ?  
21  1  3  F  .  HOH  B  201  .  ?        1  
22  1  3  F  .  HOH  B  202  .  ?        ?  
#
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  tt         ?      ?  ?          13  18.800     8  0.63    11  0.76  molprobity  1.000  
 2   2  m-85  -129.8  120.4  Favored     9  14.060    13  0.27    18  0.40  molprobity  1.000  
 3   3  m-85  -129.8  120.4  Favored     9  14.060    13  0.27    18  0.40  molprobity  1.000  
 4   4  mt    -127.9  123.9  Favored    11  10.060     8  0.36    11  0.46  molprobity  1.000  
 5   5  tt0   -134.0  124.6  Favored     8  11.690     9  0.36    12  0.43  molprobity  1.000  
 6   6  m-20  -114.3  115.8  Favored     6   9.950     8  0.25    11  0.52  molprobity  1.000  
 7   7  tp         ?      ?  ?           9  26.470     8  0.22     8  0.77  molprobity  0.931  
 8   8  tp         ?      ?  ?           9  26.470     8  0.22     8  0.77  molprobity  0.931  
 9   9  tp         ?      ?  ?          13  14.440     8  0.64    11  0.65  molprobity  1.000  
10  10  t80   -117.1  127.8  Favored     9  12.150    13  0.24    18  0.39  molprobity  1.000  
11  11  mt    -132.1  123.5  Favored    11   8.590     8  0.26    11  0.51  molprobity  1.000  
12  12  tt0   -132.8  129.6  Favored     8  10.970     9  0.28    12  0.48  molprobity  1.000  
13  13  m-80  -119.5  119.8  Favored     6   9.910     8  0.24    11  0.46  molprobity  1.000  
14  14  pt?        ?      ?  ?          11  24.510     8  0.18     8  0.59  molprobity  1.000  
15  15  ?          ?      ?  ?           6  23.100     2  0.45     1  0.22  mogul       1.000  
16  16  ?          ?      ?  ?           6  23.100     2  0.45     1  0.20  mogul       1.000  
17  17  ?          ?      ?  ?           6  48.750     2  0.45     1  0.30  mogul       1.000  
18  18  ?          ?      ?  ?           ?  29.240     ?     ?     ?     ?  ?           1.000  
19  19  ?          ?      ?  ?           ?  40.560     ?     ?     ?     ?  ?           1.000  
20  20  ?          ?      ?  ?           ?  41.310     ?     ?     ?     ?  ?           1.000  
21  21  ?          ?      ?  ?           ?  42.780     ?     ?     ?     ?  ?           1.000  
22  22  ?          ?      ?  ?           ?  34.560     ?     ?     ?     ?  ?           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  HD21  1  0.49  1.94  
2   4  HD11  1  0.49  1.94  
3   9  N     2  0.45  2.49  
4  21  O     2  0.45  2.49  
#
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   8  0.901  0.110   0.332  
 2   2  21  0.903  0.123   0.930  
 3   3  21  0.903  0.123   0.930  
 4   4   8  0.927  0.090  -0.193  
 5   5   9  0.931  0.097  -0.280  
 6   6   8  0.917  0.089  -0.213  
 7   7  13  0.916  0.216   3.107  
 8   8  13  0.916  0.216   3.107  
 9   9   8  0.941  0.094  -0.086  
10  10  12  0.935  0.096   0.198  
11  11   8  0.942  0.087  -0.273  
12  12   9  0.906  0.096  -0.296  
13  13   8  0.939  0.080  -0.373  
14  14   9  0.809  0.158   1.589  
15  15   6  0.857  0.165       ?  
16  16   6  0.857  0.165       ?  
17  17   3  0.593  0.296       ?  
18  18   1  0.769  0.197       ?  
19  19   1  0.525  0.248       ?  
20  20   1  0.736  0.290       ?  
21  21   1  0.719  0.712       ?  
22  22   1  0.872  0.129       ?  
#
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        "1.8.4, CSD as541be (2020)"                                           Y  
3  eds          2.37.1                                                                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  
##
