data_7TMA

_audit_conform.dict_name      mmcif_pdbx_vrpt.dic
_audit_conform.dict_version   0.066
_audit_conform.dict_location  https://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx_vrpt.dic
#
_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7TMA
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7TMA
_pdbx_vrpt_summary.PDB_deposition_date         2022-01-19
_pdbx_vrpt_summary.PDB_revision_number         5
_pdbx_vrpt_summary.PDB_revision_date           2024-09-25
_pdbx_vrpt_summary.report_creation_date        2024-09-17:14:04
_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      "bipyridyl-conjugated helical peptide"  
2  non-polymer  ACETONITRILE  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  2  
D  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  1.0  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   57.48  180529     ?     ?  
 2  2  1   37.78    1363  0.96  1.04  
 3  1  2  100.00  177936     ?     ?  
 4  2  2  100.00    1301  0.96  1.04  
 5  1  3  100.00  177891     ?     ?  
 6  2  3  100.00    1302  0.96  1.04  
 7  1  4  100.00  164620     ?     ?  
 8  2  4  100.00    1203  0.96  1.04  
 9  1  5   93.39  164625     ?     ?  
10  2  5   19.96    1205  0.96  1.04  
#
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  
#
_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      0.56
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.38
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   53
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  69
#
_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                     4.42
_pdbx_vrpt_summary_geometry.num_H_reduce                   89
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 53
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.38
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                69
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.56
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            106.805
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         5.255
_pdbx_vrpt_summary_diffraction.I_over_sigma              0.34(1.00A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        5364
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.402
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.481
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.317
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.964
_pdbx_vrpt_summary_diffraction.DCC_R                     0.1577
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.1762
_pdbx_vrpt_summary_diffraction.EDS_R                     0.1652
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.00
_pdbx_vrpt_summary_diffraction.EDS_res_low               13.55
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[6.512,4.279,5.033,0.000,-0.272,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.423
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 27.78 % 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 2.0675e-03. 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         8
_pdbx_vrpt_summary_diffraction.centric_outliers          1
_pdbx_vrpt_summary_diffraction.data_completeness         89.80
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      4858
_pdbx_vrpt_summary_diffraction.percent_free_reflections  9.98
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        13.55
_pdbx_vrpt_summary_diffraction.PDB_R                     0.16
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.18
_pdbx_vrpt_summary_diffraction.density_fitness_version   1.0.11
_pdbx_vrpt_summary_diffraction.CCP4_version              "9.0.002 (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_clashes
_pdbx_vrpt_model_instance.count_mogul_torsion_outliers
 1  1  1  A   1  I6W  A    1  A  ?        2     ?  
 2  1  1  A   1  I6W  A    1  B  ?        ?     ?  
 3  1  1  A   2  LEU  A    2  .  ?        ?     ?  
 4  1  1  A   3  AIB  A    3  .  ?        ?     ?  
 5  1  1  A   4  ALA  A    4  .  ?        ?     ?  
 6  1  1  A   5  MET  A    5  A  ?        ?     ?  
 7  1  1  A   5  MET  A    5  B  ?        ?     ?  
 8  1  1  A   6  LEU  A    6  .  ?        ?     ?  
 9  1  1  A   7  AIB  A    7  .  ?        ?     1  
10  1  1  A   8  GLN  A    8  .  ?        ?     ?  
11  1  1  A   9  AIB  A    9  .  ?        ?     ?  
12  1  1  A  10  LEU  A   10  .  ?        ?     ?  
13  1  1  A  11  I77  A   11  .  ?        ?     ?  
14  1  2  B   .  CCN  A  201  .  ?        ?     ?  
15  1  2  C   .  CCN  A  202  .  ?        ?     ?  
16  1  3  D   .  HOH  A  301  .  ?        ?     ?  
17  1  3  D   .  HOH  A  302  .  ?        ?     ?  
18  1  3  D   .  HOH  A  303  .  ?        ?     ?  
19  1  3  D   .  HOH  A  304  .  ?        ?     ?  
20  1  3  D   .  HOH  A  305  .  ?        ?     ?  
21  1  3  D   .  HOH  A  306  .  ?        ?     ?  
22  1  3  D   .  HOH  A  307  .  ?        ?     ?  
#
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  ?         ?      ?  ?           ?  10.290     ?     ?     ?     ?  ?           0.500  
 2   2  ?         ?      ?  ?           ?  10.290     ?     ?     ?     ?  ?           0.500  
 3   3  tp        ?      ?  ?          10   9.400     7  0.37     8  0.44  molprobity  1.000  
 4   4  ?         ?      ?  ?           7   7.160     1  0.99     0     ?  mogul       1.000  
 5   5  ?     -59.8  -34.7  Favored     5   8.080     5  0.37     7  0.45  molprobity  1.000  
 6   6  mtt   -72.4  -17.5  Favored     9   5.140     8  0.35    10  0.58  molprobity  0.500  
 7   7  mtt   -72.4  -17.5  Favored     9   5.140     8  0.35    10  0.58  molprobity  0.500  
 8   8  mt    -93.6  -43.6  Favored    10   8.760     7  0.42     8  0.29  molprobity  1.000  
 9   9  ?         ?      ?  ?           7   7.260     1  1.16     0     ?  mogul       1.000  
10  10  pt20  -50.4  -30.3  Favored     8   6.000     8  0.54     9  0.62  molprobity  1.000  
11  11  ?         ?      ?  ?           7   6.470     1  1.08     0     ?  mogul       1.000  
12  12  mt        ?      ?  ?          11   7.930     7  0.23     8  0.71  molprobity  1.000  
13  13  ?         ?      ?  ?           ?   8.610     ?     ?     ?     ?  ?           1.000  
14  14  ?         ?      ?  ?           3   8.190     2  0.78     1  0.60  mogul       1.000  
15  15  ?         ?      ?  ?           3  17.400     2  0.75     1  0.35  mogul       1.000  
16  16  ?         ?      ?  ?           ?  25.370     ?     ?     ?     ?  ?           1.000  
17  17  ?         ?      ?  ?           ?  29.330     ?     ?     ?     ?  ?           1.000  
18  18  ?         ?      ?  ?           ?  37.490     ?     ?     ?     ?  ?           1.000  
19  19  ?         ?      ?  ?           ?  38.280     ?     ?     ?     ?  ?           1.000  
20  20  ?         ?      ?  ?           ?  56.280     ?     ?     ?     ?  ?           1.000  
21  21  ?         ?      ?  ?           ?  54.000     ?     ?     ?     ?  ?           1.000  
22  22  ?         ?      ?  ?           ?  30.740     ?     ?     ?     ?  ?           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  O17  1  0.49  2.60  
2  1  C16  1  0.49  2.60  
#
_pdbx_vrpt_instance_mogul_torsion_outliers.ordinal        1
_pdbx_vrpt_instance_mogul_torsion_outliers.instance_id    9
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_1         O
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_2         C
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_3         CA
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_4         CB2
_pdbx_vrpt_instance_mogul_torsion_outliers.obsval         -84.50
_pdbx_vrpt_instance_mogul_torsion_outliers.mean           45.68
_pdbx_vrpt_instance_mogul_torsion_outliers.numobs         50
_pdbx_vrpt_instance_mogul_torsion_outliers.stdev          25.12
_pdbx_vrpt_instance_mogul_torsion_outliers.mindiff        3.04
_pdbx_vrpt_instance_mogul_torsion_outliers.local_density  4.00
#
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  60  0.947  0.111       ?  0.538   37.720  
 2   2  60  0.947  0.111       ?  0.538   37.720  
 3   3  19  0.979  0.051  -0.068  0.906  100.000  
 4   4  13  0.984  0.041       ?  0.892  100.000  
 5   5  10  0.988  0.043  -0.196  0.832   60.000  
 6   6  34  0.985  0.056  -0.011  0.381   50.000  
 7   7  34  0.985  0.056  -0.011  0.381   50.000  
 8   8  19  0.986  0.045  -0.323  0.853   62.500  
 9   9  13  0.987  0.042       ?  0.911  100.000  
10  10  17  0.980  0.042  -0.609  0.856   66.670  
11  11  13  0.990  0.032       ?  0.835   66.670  
12  12  19  0.985  0.040  -0.536  0.882  100.000  
13  13  28  0.971  0.056       ?  0.908  100.000  
14  14   6  0.983  0.040       ?  0.915  100.000  
15  15   6  0.884  0.119       ?  0.757    0.000  
16  16   1  0.950  0.097       ?  0.627    0.000  
17  17   1  0.938  0.092       ?  0.741    0.000  
18  18   1  0.886  0.150       ?  0.274    0.000  
19  19   1  0.755  0.220       ?  0.359    0.000  
20  20   1  0.633  0.252       ?  0.042    0.000  
21  21   1  0.714  0.150       ?  0.037    0.000  
22  22   1  0.902  0.084       ?  0.688    0.000  
#
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          '"2.27  (2023-04-10)"'                                                Y  
5  xtriage      1.20.1                                                                Y  
6  percentiles  "20231227.v01 (using entries in the PDB archive December 27th 2023)"  Y  
##
