data_7TMI

_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  7TMI
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7TMI
_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  2  
E  2  
F  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  0.8  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   59.51  180529     ?     ?  
 2  2  1   48.24    1424  0.60  1.00  
 3  1  2  100.00  177936     ?     ?  
 4  2  2  100.00    1340  0.60  1.00  
 5  1  3  100.00  177891     ?     ?  
 6  2  3  100.00    1341  0.60  1.00  
 7  1  4  100.00  164620     ?     ?  
 8  2  4  100.00    1276  0.60  1.00  
 9  1  5   99.95  164625     ?     ?  
10  2  5   95.69    1279  0.60  1.00  
#
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      0.45
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.30
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   48
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  64
#
_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                     4.18
_pdbx_vrpt_summary_geometry.num_H_reduce                   85
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 48
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.30
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                64
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.45
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            158.716
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         3.573
_pdbx_vrpt_summary_diffraction.I_over_sigma              9.86(0.74A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        11918
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.542
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.495
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.330
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.957
_pdbx_vrpt_summary_diffraction.DCC_R                     0.0972
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.1126
_pdbx_vrpt_summary_diffraction.EDS_R                     0.1067
_pdbx_vrpt_summary_diffraction.EDS_res_high              0.80
_pdbx_vrpt_summary_diffraction.EDS_res_low               13.37
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[4.821,3.725,2.372,0.000,0.122,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.673
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 43.61 % 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 1.7196e-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          0
_pdbx_vrpt_summary_diffraction.data_completeness         95.53
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      9337
_pdbx_vrpt_summary_diffraction.percent_free_reflections  9.90
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       0.80
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        13.37
_pdbx_vrpt_summary_diffraction.PDB_R                     0.10
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.11
_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
 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  HIS  A    5  .  ?        ?  
 7  1  1  A   6  LEU  A    6  .  ?        ?  
 8  1  1  A   7  AIB  A    7  .  ?        ?  
 9  1  1  A   8  GLN  A    8  .  ?        ?  
10  1  1  A   9  AIB  A    9  .  ?        ?  
11  1  1  A  10  LEU  A   10  .  ?        ?  
12  1  1  A  11  I77  A   11  A  ?        ?  
13  1  1  A  11  I77  A   11  B  ?        ?  
14  1  2  B   .  CCN  A  201  .  ?        ?  
15  1  2  C   .  CCN  A  202  .  ?        ?  
16  1  2  D   .  CCN  A  203  .  ?        ?  
17  1  2  E   .  CCN  A  204  .  ?        ?  
18  1  3  F   .  HOH  A  301  .  ?        ?  
19  1  3  F   .  HOH  A  302  .  ?        ?  
20  1  3  F   .  HOH  A  303  .  ?        ?  
21  1  3  F   .  HOH  A  304  .  ?        ?  
#
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  ?         ?      ?  ?           ?   4.360     ?     ?     ?     ?  ?           0.500  
 2   2  ?         ?      ?  ?           ?   4.360     ?     ?     ?     ?  ?           0.500  
 3   3  tp        ?      ?  ?          10   4.490     7  0.32     8  0.47  molprobity  1.000  
 4   4  ?         ?      ?  ?           7   3.250     1  1.14     0     ?  mogul       1.000  
 5   5  ?     -61.8  -36.1  Favored     5   4.280     5  0.37     7  0.47  molprobity  1.000  
 6   6  m80   -66.8  -20.8  Favored     7   5.000    11  0.21    15  0.30  molprobity  1.000  
 7   7  mt    -92.9  -45.5  Favored    11   4.410     7  0.37     8  0.44  molprobity  1.000  
 8   8  ?         ?      ?  ?           7   3.770     1  1.22     0     ?  mogul       1.000  
 9   9  pt20  -56.1  -25.4  Favored     8   2.580     8  0.33     9  0.33  molprobity  1.000  
10  10  ?         ?      ?  ?           7   2.730     1  1.13     0     ?  mogul       1.000  
11  11  mt        ?      ?  ?          11   4.250     7  0.27     8  0.65  molprobity  1.000  
12  12  ?         ?      ?  ?           ?   1.850     ?     ?     ?     ?  ?           0.500  
13  13  ?         ?      ?  ?           ?   1.850     ?     ?     ?     ?  ?           0.500  
14  14  ?         ?      ?  ?           3   7.060     2  0.69     1  0.46  mogul       1.000  
15  15  ?         ?      ?  ?           3   4.700     2  0.62     1  0.46  mogul       1.000  
16  16  ?         ?      ?  ?           3  26.920     2  0.89     1  0.63  mogul       1.000  
17  17  ?         ?      ?  ?           3  29.730     2  0.89     1  0.60  mogul       1.000  
18  18  ?         ?      ?  ?           ?  46.860     ?     ?     ?     ?  ?           1.000  
19  19  ?         ?      ?  ?           ?  25.250     ?     ?     ?     ?  ?           1.000  
20  20  ?         ?      ?  ?           ?   9.890     ?     ?     ?     ?  ?           1.000  
21  21  ?         ?      ?  ?           ?  29.880     ?     ?     ?     ?  ?           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  0.46  2.62  
2  1  C16  1  0.46  2.62  
#
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  0.934  0.143       ?  0.211    6.840  
 2   2  60  0.934  0.143       ?  0.211    6.840  
 3   3  18  0.991  0.040  -0.536  0.626   12.500  
 4   4  13  0.996  0.021       ?  0.677   16.670  
 5   5  10  0.988  0.047  -0.039  0.678   40.000  
 6   6  17  0.984  0.066   0.373  0.624   10.000  
 7   7  19  0.997  0.021  -1.345  0.688   25.000  
 8   8  13  0.995  0.026       ?  0.669   16.670  
 9   9  17  0.998  0.017  -1.252  0.669   33.330  
10  10  13  0.996  0.021       ?  0.670   16.670  
11  11  19  0.992  0.039  -0.579  0.655   12.500  
12  12  56  0.967  0.069       ?  0.588    4.220  
13  13  56  0.967  0.069       ?  0.588    4.220  
14  14   6  0.958  0.139       ?  0.632   33.330  
15  15   6  0.990  0.068       ?  0.686   33.330  
16  16   6  0.873  0.123       ?  0.297    0.000  
17  17   6  0.844  0.143       ?  0.431    0.000  
18  18   1  0.815  0.165       ?  0.039    0.000  
19  19   1  0.867  0.147       ?  0.699    0.000  
20  20   1  0.981  0.055       ?  0.847  100.000  
21  21   1  0.653  0.251       ?  0.234    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  
##
