data_9DYY

_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  9DYY
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    9DYY
_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        2025-03-16:18:04
_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      VVGG(DVA)(DVA)                     
2  non-polymer  1,1,1,3,3,3-hexafluoropropan-2-ol  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  1  
D  1  
E  2  
F  2  
G  2  
H  2  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  1.3  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    1497  1.30  1.30  
 3  1  2  100.00  177936     ?     ?  
 4  2  2  100.00    1455  1.30  1.30  
 5  1  3  100.00  177891     ?     ?  
 6  2  3  100.00    1455  1.30  1.30  
 7  1  4  100.00  164620     ?     ?  
 8  2  4  100.00    1384  1.30  1.30  
 9  1  5   89.55  164625     ?     ?  
10  2  5   41.08    1387  1.30  1.30  
#
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  
13  3  2  C  1  1  C  100.00  
14  4  2  C  1  1  C  100.00  
15  5  3  C  1  1  C  100.00  
16  6  3  C  1  1  C  100.00  
17  7  4  C  1  1  C  100.00  
18  8  4  C  1  1  C  100.00  
19  3  2  D  1  1  D  100.00  
20  4  2  D  1  1  D  100.00  
21  5  3  D  1  1  D  100.00  
22  6  3  D  1  1  D  100.00  
23  7  4  D  1  1  D  100.00  
24  8  4  D  1  1  D  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  0.45  21  27  
2  1  1  B  B  0.75  0.38  21  27  
3  1  1  C  C  0.79  0.46  21  27  
4  1  1  D  D  0.67  0.46  21  27  
#
_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                   176
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 84
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.44
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                108
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.72
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            349.402
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         10.113
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.01(1.30A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3741
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            1.004
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.542
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.401
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.978
_pdbx_vrpt_summary_diffraction.DCC_R                     0.1834
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.1933
_pdbx_vrpt_summary_diffraction.EDS_R                     0.1852
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.30
_pdbx_vrpt_summary_diffraction.EDS_res_low               26.52
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[16.497,9.823,7.110,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.842
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 78.74 % 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 6.4933e-07. 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         12
_pdbx_vrpt_summary_diffraction.centric_outliers          4
_pdbx_vrpt_summary_diffraction.data_completeness         99.52
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      374
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.00
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.30
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        26.52
_pdbx_vrpt_summary_diffraction.PDB_R                     0.1810
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.1880
_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
_pdbx_vrpt_model_instance.count_mogul_torsion_outliers
 1  1  1  A  1  VAL  A    1  .  ?        ?  
 2  1  1  A  2  VAL  A    2  .  ?        ?  
 3  1  1  A  3  GLY  A    3  .  ?        ?  
 4  1  1  A  4  GLY  A    4  .  ?        ?  
 5  1  1  A  5  DVA  A    5  .  ?        ?  
 6  1  1  A  6  DVA  A    6  .  ?        ?  
 7  1  1  A  7  NH2  A    7  .  ?        ?  
 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  DVA  B    5  .  ?        ?  
13  1  1  B  6  DVA  B    6  .  ?        ?  
14  1  1  B  7  NH2  B    7  .  ?        ?  
15  1  1  C  1  VAL  C    1  .  ?        ?  
16  1  1  C  2  VAL  C    2  .  ?        ?  
17  1  1  C  3  GLY  C    3  .  ?        ?  
18  1  1  C  4  GLY  C    4  .  ?        ?  
19  1  1  C  5  DVA  C    5  .  ?        ?  
20  1  1  C  6  DVA  C    6  .  ?        ?  
21  1  1  C  7  NH2  C    7  .  ?        ?  
22  1  1  D  1  VAL  D    1  .  ?        ?  
23  1  1  D  2  VAL  D    2  .  ?        ?  
24  1  1  D  3  GLY  D    3  .  ?        ?  
25  1  1  D  4  GLY  D    4  .  ?        ?  
26  1  1  D  5  DVA  D    5  .  ?        ?  
27  1  1  D  6  DVA  D    6  .  ?        ?  
28  1  1  D  7  NH2  D    7  .  ?        ?  
29  1  2  E  .  CFH  C  101  .  ?        ?  
30  1  2  F  .  CFH  C  102  .  ?        6  
31  1  2  G  .  CFH  D  101  .  ?        ?  
32  1  2  H  .  CFH  D  102  .  ?        ?  
#
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  t          ?       ?  ?          11  12.910     7  0.69    10  0.73  molprobity  1.000  
 2   2  m     -139.2   161.2  Favored     9   9.260     7  0.20    10  0.58  molprobity  1.000  
 3   3  ?     -164.3   155.5  Favored     3   8.600     4  0.21     5  0.74  molprobity  1.000  
 4   4  ?     -176.6   179.2  Favored     3   7.860     3  0.42     2  0.33  molprobity  1.000  
 5   5  ?          ?       ?  ?           8   9.950     ?     ?     ?     ?  ?           1.000  
 6   6  ?          ?       ?  ?           8  14.710     ?     ?     ?     ?  ?           1.000  
 7   7  ?          ?       ?  ?           ?  13.730     ?     ?     ?     ?  ?           1.000  
 8   8  m          ?       ?  ?          11  11.790     7  0.54    10  0.79  molprobity  1.000  
 9   9  t     -141.0   142.0  Favored     9  10.700     7  0.16    10  0.86  molprobity  1.000  
10  10  ?     -166.8   166.7  Favored     3   8.240     4  0.28     5  0.52  molprobity  1.000  
11  11  ?      172.9  -168.8  Favored     3   8.060     3  0.41     2  0.35  molprobity  1.000  
12  12  ?          ?       ?  ?           8   9.610     ?     ?     ?     ?  ?           1.000  
13  13  ?          ?       ?  ?           8  12.590     ?     ?     ?     ?  ?           1.000  
14  14  ?          ?       ?  ?           ?  11.380     ?     ?     ?     ?  ?           1.000  
15  15  m          ?       ?  ?          11  11.920     7  0.67    10  0.54  molprobity  1.000  
16  16  t     -148.3   138.7  Favored     9  11.460     7  0.20    10  1.07  molprobity  1.000  
17  17  ?      177.7   179.0  Favored     3   9.670     4  0.26     5  0.38  molprobity  1.000  
18  18  ?      149.4  -152.7  Favored     3   8.870     3  0.51     2  0.90  molprobity  1.000  
19  19  ?          ?       ?  ?           8  10.480     ?     ?     ?     ?  ?           1.000  
20  20  ?          ?       ?  ?           8  11.720     ?     ?     ?     ?  ?           1.000  
21  21  ?          ?       ?  ?           ?  11.790     ?     ?     ?     ?  ?           1.000  
22  22  t          ?       ?  ?          11  14.070     7  0.69    10  0.71  molprobity  1.000  
23  23  m     -136.5   154.6  Favored     9  11.310     7  0.20    10  0.58  molprobity  1.000  
24  24  ?     -158.6   153.1  Favored     3   8.840     4  0.26     5  0.81  molprobity  1.000  
25  25  ?      179.2  -175.4  Favored     3   8.260     3  0.39     2  0.44  molprobity  1.000  
26  26  ?          ?       ?  ?           8  10.800     ?     ?     ?     ?  ?           1.000  
27  27  ?          ?       ?  ?           8  12.200     ?     ?     ?     ?  ?           1.000  
28  28  ?          ?       ?  ?           ?  13.190     ?     ?     ?     ?  ?           1.000  
29  29  ?          ?       ?  ?           2  25.040     9  0.40    15  0.37  mogul       1.000  
30  30  ?          ?       ?  ?           2  30.750     9  0.26    15  0.39  mogul       1.000  
31  31  ?          ?       ?  ?           2  19.120     9  0.33    15  0.30  mogul       1.000  
32  32  ?          ?       ?  ?           2  20.190     9  0.46    15  0.56  mogul       1.000  
#
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  30  C1  C2  C3  F10   35.46  62.84  759  53.62  2.68  1.32  
2  30  C1  C2  C3  F8   -83.97  45.45  759  31.86  1.56  2.11  
3  30  C1  C2  C3  F9   155.78  69.38  759  36.97  4.86  1.05  
4  30  O4  C2  C3  F10  155.82  70.23  780  37.28  0.94  1.15  
5  30  O4  C2  C3  F8    36.39  61.45  780  54.14  0.05  1.15  
6  30  O4  C2  C3  F9   -83.86  46.27  780  31.59  4.03  1.15  
#
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  0.960  0.055  -0.008  0.786   57.140  
 2   2  16  0.977  0.039  -0.643  0.900   85.710  
 3   3   7  0.962  0.037  -0.540  0.904  100.000  
 4   4   7  0.965  0.054  -0.021  0.881   75.000  
 5   5  16  0.967  0.056       ?  0.746   57.140  
 6   6  16  0.959  0.070       ?  0.560   57.140  
 7   7   3  0.988  0.030       ?  0.796    0.000  
 8   8  18  0.946  0.060   0.190  0.808   85.710  
 9   9  16  0.973  0.046  -0.365  0.867   71.430  
10  10   7  0.977  0.044  -0.326  0.935  100.000  
11  11   7  0.984  0.032  -0.692  0.914  100.000  
12  12  16  0.974  0.048       ?  0.693   57.140  
13  13  16  0.968  0.065       ?  0.646   42.860  
14  14   3  0.982  0.075       ?  0.745    0.000  
15  15  18  0.972  0.047  -0.325  0.747   42.860  
16  16  16  0.967  0.045  -0.405  0.800   71.430  
17  17   7  0.981  0.036  -0.570  0.892   75.000  
18  18   7  0.976  0.035  -0.601  0.868   75.000  
19  19  16  0.979  0.046       ?  0.802   57.140  
20  20  16  0.970  0.062       ?  0.677   28.570  
21  21   3  0.984  0.039       ?  0.707    0.000  
22  22  18  0.928  0.076   0.825  0.796   57.140  
23  23  16  0.960  0.066   0.429  0.879   85.710  
24  24   7  0.947  0.045  -0.296  0.946  100.000  
25  25   7  0.974  0.055   0.009  0.892  100.000  
26  26  16  0.952  0.061       ?  0.677   71.430  
27  27  16  0.965  0.055       ?  0.785   57.140  
28  28   3  0.974  0.118       ?  0.720    0.000  
29  29  11  0.950  0.078       ?  0.667   70.000  
30  30  11  0.897  0.114       ?  0.434   40.000  
31  31  11  0.973  0.046       ?  0.951  100.000  
32  32  11  0.942  0.073       ?  0.872   80.000  
#
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  mogul        "2022.3.0, CSD as543be (2022)"                                        Y  
3  eds          3.0                                                                   Y  
4  dcc          '"2.29  (2024-07-11))"'                                               Y  
5  xtriage      1.21                                                                  Y  
6  percentiles  "20231227.v01 (using entries in the PDB archive December 27th 2023)"  Y  
##
