data_6N5T

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  6N5T
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    6N5T
_pdbx_vrpt_summary.PDB_deposition_date         2018-11-22
_pdbx_vrpt_summary.PDB_revision_number         2
_pdbx_vrpt_summary.PDB_revision_date           2023-10-11
_pdbx_vrpt_summary.report_creation_date        2023-10-02:11:39
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,mogul,buster-report,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   Y
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "RNA (126-MER)"  
2  non-polymer  "(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide"  
3  non-polymer  "MAGNESIUM ION"  
4  non-polymer  "POTASSIUM ION"  
5  non-polymer  "SULFATE ION"  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  2  
D  3  
E  3  
F  4  
G  3  
H  3  
I  5  
#
_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_diffraction.exp_method              x-ray
_pdbx_vrpt_summary_diffraction.ordinal                 1
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate       93.077
_pdbx_vrpt_summary_diffraction.I_over_sigma            1.15(2.77A)
_pdbx_vrpt_summary_diffraction.num_miller_indices      21721
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean   0.502
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean  0.336
_pdbx_vrpt_summary_diffraction.twin_fraction           -h,-k,l:0.015
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso          "[106.625,106.625,72.910,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy         0.353
_pdbx_vrpt_summary_diffraction.trans_NCS_details       "The largest off-origin peak in the Patterson function is 6.70% of the height of the origin peak. No significant pseudotranslation is detected."
_pdbx_vrpt_summary_diffraction.acentric_outliers       3
_pdbx_vrpt_summary_diffraction.centric_outliers        2
_pdbx_vrpt_summary_diffraction.PDB_resolution_high     2.79
_pdbx_vrpt_summary_diffraction.PDB_resolution_low      74.83
_pdbx_vrpt_summary_diffraction.PDB_R                   0.18
_pdbx_vrpt_summary_diffraction.PDB_Rfree               0.20
#
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  GTP  A    1  .  ?        ?     ?     ?  
  2  1  1  A    2  G    A    2  .  ?        ?     ?     ?  
  3  1  1  A    3  U    A    3  .  ?        ?     ?     ?  
  4  1  1  A    4  U    A    4  .  ?        ?     ?     ?  
  5  1  1  A    5  G    A    5  .  ?        ?     ?     ?  
  6  1  1  A    6  C    A    6  .  ?        ?     ?     ?  
  7  1  1  A    7  C    A    7  .  ?        ?     ?     ?  
  8  1  1  A    8  G    A    8  .  ?        ?     ?     ?  
  9  1  1  A    9  A    A    9  .  ?        ?     ?     ?  
 10  1  1  A   10  A    A   10  .  ?        ?     ?     ?  
 11  1  1  A   11  U    A   11  .  ?        ?     ?     ?  
 12  1  1  A   12  C    A   12  .  ?        ?     ?     ?  
 13  1  1  A   13  C    A   13  .  ?        ?     ?     ?  
 14  1  1  A   14  C    A   14  .  ?        ?     ?     ?  
 15  1  1  A   15  C    A   15  .  ?        ?     ?     ?  
 16  1  1  A   16  U    A   16  .  ?        ?     ?     ?  
 17  1  1  A   17  A    A   17  .  ?        ?     ?     ?  
 18  1  1  A   18  G    A   18  .  ?        ?     ?     ?  
 19  1  1  A   19  A    A   19  .  ?        ?     ?     ?  
 20  1  1  A   20  A    A   20  .  ?        ?     ?     ?  
 21  1  1  A   21  A    A   21  .  ?        ?     ?     ?  
 22  1  1  A   22  G    A   22  .  ?        ?     ?     ?  
 23  1  1  A   23  G    A   23  .  ?        ?     ?     ?  
 24  1  1  A   24  U    A   24  .  ?        ?     ?     ?  
 25  1  1  A   25  A    A   25  .  ?        ?     ?     ?  
 26  1  1  A   26  C    A   26  .  ?        ?     ?     ?  
 27  1  1  A   27  G    A   27  .  ?        ?     ?     ?  
 28  1  1  A   28  G    A   28  .  ?        ?     ?     ?  
 29  1  1  A   29  A    A   29  .  ?        ?     ?     ?  
 30  1  1  A   30  G    A   30  .  ?        ?     ?     ?  
 31  1  1  A   31  G    A   31  .  ?        ?     ?     ?  
 32  1  1  A   32  A    A   32  .  ?        ?     ?     ?  
 33  1  1  A   33  A    A   33  .  ?        ?     ?     ?  
 34  1  1  A   34  C    A   34  .  ?        ?     ?     ?  
 35  1  1  A   35  C    A   35  .  ?        ?     ?     ?  
 36  1  1  A   36  G    A   36  .  ?        ?     ?     ?  
 37  1  1  A   37  C    A   37  .  ?        ?     ?     ?  
 38  1  1  A   38  U    A   38  .  ?        ?     ?     ?  
 39  1  1  A   39  U    A   39  .  ?        ?     ?     ?  
 40  1  1  A   40  U    A   40  .  ?        ?     ?     ?  
 41  1  1  A   41  U    A   41  .  ?        ?     ?     ?  
 42  1  1  A   42  U    A   42  .  ?        ?     ?     ?  
 43  1  1  A   43  G    A   43  .  ?        ?     ?     ?  
 44  1  1  A   44  G    A   44  .  ?        ?     ?     ?  
 45  1  1  A   45  G    A   45  .  ?        ?     ?     ?  
 46  1  1  A   46  G    A   46  .  ?        ?     ?     ?  
 47  1  1  A   47  U    A   47  .  ?        ?     ?     ?  
 48  1  1  A   48  U    A   48  .  ?        ?     ?     ?  
 49  1  1  A   49  A    A   49  .  ?        ?     ?     ?  
 50  1  1  A   50  A    A   50  .  ?        ?     ?     ?  
 51  1  1  A   51  U    A   51  .  ?        ?     ?     ?  
 52  1  1  A   52  C    A   52  .  ?        ?     ?     ?  
 53  1  1  A   53  U    A   53  .  ?        ?     ?     ?  
 54  1  1  A   54  G    A   54  .  ?        ?     ?     ?  
 55  1  1  A   55  C    A   55  .  ?        ?     ?     ?  
 56  1  1  A   56  A    A   56  .  ?        ?     ?     ?  
 57  1  1  A   57  G    A   57  .  ?        ?     ?     ?  
 58  1  1  A   58  U    A   58  .  ?        ?     ?     ?  
 59  1  1  A   59  G    A   59  .  ?        ?     ?     ?  
 60  1  1  A   60  A    A   60  .  ?        ?     ?     ?  
 61  1  1  A   61  A    A   61  .  ?        ?     ?     ?  
 62  1  1  A   62  G    A   62  .  ?        ?     ?     ?  
 63  1  1  A   63  C    A   63  .  ?        ?     ?     ?  
 64  1  1  A   64  U    A   64  .  ?        ?     ?     ?  
 65  1  1  A   65  G    A   65  .  ?        ?     ?     ?  
 66  1  1  A   66  C    A   66  .  ?        ?     ?     ?  
 67  1  1  A   67  A    A   67  .  ?        ?     ?     ?  
 68  1  1  A   68  G    A   68  .  ?        ?     ?     ?  
 69  1  1  A   69  U    A   69  .  ?        ?     ?     ?  
 70  1  1  A   70  A    A   70  .  ?        ?     ?     ?  
 71  1  1  A   71  G    A   71  .  ?        ?     ?     ?  
 72  1  1  A   72  G    A   72  .  ?        ?     ?     ?  
 73  1  1  A   73  G    A   73  .  ?        ?     ?     ?  
 74  1  1  A   74  A    A   74  .  ?        ?     ?     ?  
 75  1  1  A   75  U    A   75  .  ?        ?     ?     ?  
 76  1  1  A   76  A    A   76  .  ?        ?     ?     ?  
 77  1  1  A   77  C    A   77  .  ?        ?     ?     ?  
 78  1  1  A   78  C    A   78  .  ?        ?     ?     ?  
 79  1  1  A   79  U    A   79  .  ?        ?     ?     ?  
 80  1  1  A   80  U    A   80  .  ?        ?     ?     ?  
 81  1  1  A   81  C    A   81  .  ?        ?     ?     ?  
 82  1  1  A   82  U    A   82  .  ?        ?     ?     ?  
 83  1  1  A   83  G    A   83  .  ?        ?     ?     ?  
 84  1  1  A   84  U    A   84  .  ?        ?     ?     ?  
 85  1  1  A   85  C    A   85  .  ?        ?     ?     ?  
 86  1  1  A   86  C    A   86  .  ?        ?     ?     ?  
 87  1  1  A   87  C    A   87  .  ?        ?     ?     ?  
 88  1  1  A   88  G    A   88  .  ?        ?     ?     ?  
 89  1  1  A   89  C    A   89  .  ?        ?     ?     ?  
 90  1  1  A   90  A    A   90  .  ?        ?     ?     ?  
 91  1  1  A   91  C    A   91  .  ?        ?     ?     ?  
 92  1  1  A   92  C    A   92  .  ?        ?     ?     ?  
 93  1  1  A   93  C    A   93  .  ?        ?     ?     ?  
 94  1  1  A   94  G    A   94  .  ?        ?     ?     ?  
 95  1  1  A   95  A    A   95  .  ?        ?     ?     ?  
 96  1  1  A   96  C    A   96  .  ?        ?     ?     ?  
 97  1  1  A   97  A    A   97  .  ?        ?     ?     ?  
 98  1  1  A   98  G    A   98  .  ?        ?     ?     ?  
 99  1  1  A   99  C    A   99  .  ?        ?     ?     ?  
100  1  1  A  100  U    A  100  .  ?        ?     ?     ?  
101  1  1  A  101  A    A  101  .  ?        ?     ?     ?  
102  1  1  A  102  A    A  102  .  ?        ?     ?     ?  
103  1  1  A  103  C    A  103  .  ?        ?     ?     ?  
104  1  1  A  104  U    A  104  .  ?        ?     ?     ?  
105  1  1  A  105  C    A  105  .  ?        ?     ?     ?  
106  1  1  A  106  C    A  106  .  ?        ?     ?     ?  
107  1  1  A  107  G    A  107  .  ?        ?     ?     ?  
108  1  1  A  108  G    A  108  .  ?        ?     ?     ?  
109  1  1  A  109  A    A  109  .  ?        ?     ?     ?  
110  1  1  A  110  G    A  110  .  ?        ?     ?     ?  
111  1  1  A  111  G    A  111  .  ?        ?     ?     ?  
112  1  1  A  112  C    A  112  .  ?        ?     ?     ?  
113  1  1  A  113  A    A  113  .  ?        ?     ?     ?  
114  1  1  A  114  A    A  114  .  ?        ?     ?     ?  
115  1  1  A  115  U    A  115  .  ?        ?     ?     ?  
116  1  1  A  116  A    A  116  .  ?        ?     ?     ?  
117  1  1  A  117  A    A  117  .  ?        ?     ?     ?  
118  1  1  A  118  A    A  118  .  ?        ?     ?     ?  
119  1  1  A  119  G    A  119  .  ?        ?     ?     ?  
120  1  1  A  120  G    A  120  .  ?        ?     ?     ?  
121  1  1  A  121  A    A  121  .  ?        ?     ?     ?  
122  1  1  A  122  A    A  122  .  ?        ?     ?     ?  
123  1  1  A  123  G    A  123  .  ?        ?     ?     ?  
124  1  1  A  124  G    A  124  .  ?        ?     ?     ?  
125  1  1  A  125  A    A  125  .  ?        ?     ?     ?  
126  1  1  A  126  G    A  126  .  ?        ?     ?     ?  
127  1  2  B    .  2BA  A  201  .  ?        2     6     5  
128  1  2  C    .  2BA  A  202  .  ?        2     6     5  
129  1  3  D    .  MG   A  203  .  ?        ?     ?     ?  
130  1  3  E    .  MG   A  204  .  ?        ?     ?     ?  
131  1  4  F    .  K    A  205  .  ?        ?     ?     ?  
132  1  3  G    .  MG   A  206  .  ?        ?     ?     ?  
133  1  3  H    .  MG   A  207  .  ?        ?     ?     ?  
134  1  5  I    .  SO4  A  208  .  ?        ?     ?     ?  
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_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
1  127  44  0.96  50  1.23  mogul  
2  128  44  0.96  50  1.21  mogul  
3  134   4  0.14   6  0.06  mogul  
#
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  127  C5   C4   1.47  1.40  24  0.03  2.48  0.00  
2  127  C51  C41  1.47  1.40  24  0.03  2.48  0.00  
3  128  C5   C4   1.47  1.40  24  0.03  2.56  0.00  
4  128  C51  C41  1.47  1.40  24  0.03  2.52  0.00  
#
loop_
_pdbx_vrpt_instance_mogul_angle_outliers.ordinal
_pdbx_vrpt_instance_mogul_angle_outliers.instance_id
_pdbx_vrpt_instance_mogul_angle_outliers.atom_1
_pdbx_vrpt_instance_mogul_angle_outliers.atom_2
_pdbx_vrpt_instance_mogul_angle_outliers.atom_3
_pdbx_vrpt_instance_mogul_angle_outliers.obsval
_pdbx_vrpt_instance_mogul_angle_outliers.mean
_pdbx_vrpt_instance_mogul_angle_outliers.numobs
_pdbx_vrpt_instance_mogul_angle_outliers.stdev
_pdbx_vrpt_instance_mogul_angle_outliers.Zscore
_pdbx_vrpt_instance_mogul_angle_outliers.mindiff
 1  127  "C3'"   "C2'"   "C1'"   105.51   99.89  267  2.22   2.54  0.36  
 2  127  C4      C5      N7      106.43  109.40   21  1.04  -2.85  1.09  
 3  127  N3      C2      N1      123.80  128.68  136  1.56  -3.12  1.38  
 4  127  "C3'1"  "C2'1"  "C1'1"  105.55   99.89  267  2.22   2.55  0.32  
 5  127  C41     C51     N71     106.77  109.40   21  1.04  -2.52  0.75  
 6  127  N31     C21     N11     123.91  128.68  136  1.56  -3.05  1.27  
 7  128  "C3'"   "C2'"   "C1'"   105.11   99.89  267  2.22   2.36  0.06  
 8  128  C4      C5      N7      106.62  109.40   21  1.04  -2.67  0.90  
 9  128  N3      C2      N1      123.82  128.68  136  1.56  -3.11  1.35  
10  128  "C3'1"  "C2'1"  "C1'1"  105.60   99.89  267  2.22   2.58  0.27  
11  128  C41     C51     N71     107.07  109.40   21  1.04  -2.23  0.44  
12  128  N31     C21     N11     123.75  128.68  136  1.56  -3.15  1.42  
#
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  127  "C5'1"  "O5'1"  P1      "O3'"    111.04  43.08  174  11.12   0.67  0.57  
 2  127  "C5'1"  "O5'1"  P1      O1P1    -135.03  65.82   43  27.15  12.01  0.00  
 3  127  "C5'1"  "O5'1"  P1      O2P1      -2.31  96.41   43  53.48  28.51  0.00  
 4  127  "O4'1"  "C4'1"  "C5'1"  "O5'1"  -104.04  39.90  451  10.25   3.07  0.44  
 5  127  "C3'1"  "C4'1"  "C5'1"  "O5'1"    15.41  54.25  451  40.99   2.26  0.44  
 6  128  "C5'1"  "O5'1"  P1      "O3'"     96.59  29.80  174  13.21   2.25  2.87  
 7  128  "C5'1"  "O5'1"  P1      O1P1    -150.48  70.03   43  40.61   3.45  4.65  
 8  128  "C5'1"  "O5'1"  P1      O2P1     -16.17  82.56   43  53.48  14.66  0.00  
 9  128  "O4'1"  "C4'1"  "C5'1"  "O5'1"   -94.83  31.67  451  12.78   2.46  1.11  
10  128  "C3'1"  "C4'1"  "C5'1"  "O5'1"    24.33  45.41  451  40.92   0.77  1.55  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  mogul        "1.8.5 (274361), CSD as541be (2020)"                                  Y  
2  xtriage      1.13                                                                  Y  
3  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  N  
##
