data_7TMH

_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  7TMH
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7TMH
_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  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   99.96  180529     ?     ?  
 2  2  1   99.86    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   99.71  164625     ?     ?  
10  2  5   78.04    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      0.56
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.32
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   77
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  98
#
_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                   115
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 77
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.32
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                98
_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            47.664
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         5.116
_pdbx_vrpt_summary_diffraction.I_over_sigma              4.11(0.75A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        11374
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.398
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.472
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.305
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.978
_pdbx_vrpt_summary_diffraction.DCC_R                     0.1162
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.1258
_pdbx_vrpt_summary_diffraction.EDS_R                     0.1193
_pdbx_vrpt_summary_diffraction.EDS_res_high              0.80
_pdbx_vrpt_summary_diffraction.EDS_res_low               13.50
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[6.167,5.230,4.142,0.000,-0.752,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.391
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 34.37 % 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 6.9027e-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         1
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         94.29
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      9188
_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       0.80
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        13.50
_pdbx_vrpt_summary_diffraction.PDB_R                     0.12
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.13
_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_mogul_bond_outliers
_pdbx_vrpt_model_instance.count_mogul_angle_outliers
_pdbx_vrpt_model_instance.count_mogul_torsion_outliers
 1  1  1  A   1  I6W  A    1  .  ?        ?     ?     ?  
 2  1  1  A   2  LEU  A    2  .  ?        ?     ?     ?  
 3  1  1  A   3  AIB  A    3  .  ?        ?     ?     ?  
 4  1  1  A   4  SER  A    4  .  ?        ?     ?     ?  
 5  1  1  A   5  PHI  A    5  A  ?        1     ?     1  
 6  1  1  A   5  PHI  A    5  B  ?        1     1     2  
 7  1  1  A   6  LEU  A    6  A  ?        ?     ?     ?  
 8  1  1  A   6  LEU  A    6  B  ?        ?     ?     ?  
 9  1  1  A   7  MET  A    7  A  ?        ?     ?     ?  
10  1  1  A   7  MET  A    7  B  ?        ?     ?     ?  
11  1  1  A   8  GLN  A    8  A  ?        ?     ?     ?  
12  1  1  A   8  GLN  A    8  B  ?        ?     ?     ?  
13  1  1  A   9  AIB  A    9  A  ?        ?     ?     ?  
14  1  1  A   9  AIB  A    9  B  ?        ?     ?     ?  
15  1  1  A  10  LEU  A   10  A  ?        ?     ?     ?  
16  1  1  A  10  LEU  A   10  B  ?        ?     ?     ?  
17  1  1  A  11  I77  A   11  .  ?        ?     ?     ?  
18  1  2  B   .  CCN  A  201  .  ?        ?     ?     ?  
19  1  2  C   .  CCN  A  202  .  ?        ?     ?     ?  
20  1  3  D   .  HOH  A  301  .  ?        ?     ?     ?  
21  1  3  D   .  HOH  A  302  .  ?        ?     ?     ?  
22  1  3  D   .  HOH  A  303  .  ?        ?     ?     ?  
23  1  3  D   .  HOH  A  304  .  ?        ?     ?     ?  
24  1  3  D   .  HOH  A  305  .  ?        ?     ?     ?  
#
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  ?         ?      ?  ?           ?  10.070     ?     ?     ?     ?  ?           1.000  
 2   2  tp        ?      ?  ?          10   6.220     7  0.33     8  0.49  molprobity  1.000  
 3   3  ?         ?      ?  ?           7   5.010     1  1.10     0     ?  mogul       1.000  
 4   4  p     -64.5  -32.0  Favored     5   5.320     5  0.22     5  0.43  molprobity  1.000  
 5   5  ?         ?      ?  ?           8   3.740    11  1.12    10  0.69  mogul       0.500  
 6   6  ?         ?      ?  ?           8   3.740    11  1.14    10  1.22  mogul       0.500  
 7   7  mt    -90.2  -40.2  Favored     ?   5.460     8  0.31    11  0.37  molprobity  1.000  
 8   8  mt    -90.2  -40.2  Favored     ?   5.460     8  0.31    11  0.37  molprobity  1.000  
 9   9  mtt   -73.2   -9.4  Favored     9   3.220     8  0.25    10  0.71  molprobity  0.500  
10  10  mtt   -73.2   -9.4  Favored     9   3.220     8  0.25    10  0.71  molprobity  0.500  
11  11  pt20  -60.4  -21.3  Favored     ?   3.800     8  0.33     9  0.31  molprobity  1.000  
12  12  pt20  -60.4  -21.3  Favored     ?   3.800     8  0.33     9  0.31  molprobity  1.000  
13  13  ?         ?      ?  ?           7   2.590     1  0.97     0     ?  mogul       0.500  
14  14  ?         ?      ?  ?           7   2.590     1  0.92     0     ?  mogul       0.500  
15  15  mt        ?      ?  ?          11   2.620     7  0.42     8  0.81  molprobity  0.500  
16  16  mt        ?      ?  ?          11   2.620     7  0.42     8  0.81  molprobity  0.500  
17  17  ?         ?      ?  ?           ?   5.080     ?     ?     ?     ?  ?           1.000  
18  18  ?         ?      ?  ?           3   7.820     2  0.75     1  0.54  mogul       1.000  
19  19  ?         ?      ?  ?           3  34.420     2  0.91     1  0.55  mogul       1.000  
20  20  ?         ?      ?  ?           ?  16.740     ?     ?     ?     ?  ?           1.000  
21  21  ?         ?      ?  ?           ?  22.580     ?     ?     ?     ?  ?           1.000  
22  22  ?         ?      ?  ?           ?  24.050     ?     ?     ?     ?  ?           1.000  
23  23  ?         ?      ?  ?           ?  20.430     ?     ?     ?     ?  ?           1.000  
24  24  ?         ?      ?  ?           ?  24.980     ?     ?     ?     ?  ?           1.000  
#
loop_
_pdbx_vrpt_instance_mogul_bond_outliers.ordinal
_pdbx_vrpt_instance_mogul_bond_outliers.instance_id
_pdbx_vrpt_instance_mogul_bond_outliers.atom_1
_pdbx_vrpt_instance_mogul_bond_outliers.atom_2
_pdbx_vrpt_instance_mogul_bond_outliers.obsval
_pdbx_vrpt_instance_mogul_bond_outliers.mean
_pdbx_vrpt_instance_mogul_bond_outliers.numobs
_pdbx_vrpt_instance_mogul_bond_outliers.stdev
_pdbx_vrpt_instance_mogul_bond_outliers.Zscore
_pdbx_vrpt_instance_mogul_bond_outliers.mindiff
1  5  CZ  I  2.03  2.10  4849  0.03  -2.53  0.00  
2  6  CZ  I  2.04  2.10  4849  0.03  -2.19  0.00  
#
_pdbx_vrpt_instance_mogul_angle_outliers.ordinal      1
_pdbx_vrpt_instance_mogul_angle_outliers.instance_id  6
_pdbx_vrpt_instance_mogul_angle_outliers.atom_1       CE2
_pdbx_vrpt_instance_mogul_angle_outliers.atom_2       CZ
_pdbx_vrpt_instance_mogul_angle_outliers.atom_3       CE1
_pdbx_vrpt_instance_mogul_angle_outliers.obsval       117.35
_pdbx_vrpt_instance_mogul_angle_outliers.mean         120.64
_pdbx_vrpt_instance_mogul_angle_outliers.numobs       2730
_pdbx_vrpt_instance_mogul_angle_outliers.stdev        1.32
_pdbx_vrpt_instance_mogul_angle_outliers.Zscore       -2.49
_pdbx_vrpt_instance_mogul_angle_outliers.mindiff      0.07
#
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  5  C   CA  CB  CG   154.44  51.72     42  36.80  6.91  2.38  
2  6  CA  CB  CG  CD1  151.34  62.03  10791  22.76  0.01  1.56  
3  6  CA  CB  CG  CD2  -28.79  61.43  10791  22.87  0.11  1.53  
#
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  30  0.970  0.074       ?  0.670    7.140  
 2   2  18  0.988  0.045  -0.323  0.822   75.000  
 3   3  13  0.992  0.038       ?  0.798   50.000  
 4   4  11  0.993  0.028  -0.829  0.797   50.000  
 5   5  40  0.986  0.095       ?  0.143   19.780  
 6   6  40  0.986  0.095       ?  0.143   19.780  
 7   7  20  0.992  0.037  -0.664  0.840   87.500  
 8   8  20  0.992  0.037  -0.664  0.840   87.500  
 9   9  34  0.989  0.044  -0.334  0.465   25.000  
10  10  34  0.989  0.044  -0.334  0.465   25.000  
11  11  18  0.994  0.025  -1.046  0.789   55.560  
12  12  18  0.994  0.025  -1.046  0.789   55.560  
13  13  26  0.979  0.051       ?  0.797   50.000  
14  14  26  0.979  0.051       ?  0.797   50.000  
15  15  38  0.990  0.037  -0.664  0.697   27.230  
16  16  38  0.990  0.037  -0.664  0.697   27.230  
17  17  28  0.987  0.042       ?  0.685   20.000  
18  18   6  0.959  0.064       ?  0.895  100.000  
19  19   6  0.581  0.148       ?  0.180    0.000  
20  20   1  0.945  0.081       ?  0.875  100.000  
21  21   1  0.940  0.055       ?  0.694    0.000  
22  22   1  0.863  0.113       ?  0.542    0.000  
23  23   1  0.874  0.099       ?  0.753    0.000  
24  24   1  0.832  0.103       ?  0.541    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  
##
