| Experiment | |
|---|---|
Method _exptl.method | X-RAY DIFFRACTION |
Experimental protocol _diffrn_radiation.pdbx_diffrn_protocol | SINGLE WAVELENGTH |
Source type _diffrn_source.source | SYNCHROTRON |
Source details _diffrn_source.type | CLSI BEAMLINE 08ID-1 |
Synchrotron site _diffrn_source.pdbx_synchrotron_site | CLSI |
Beamline _diffrn_source.pdbx_synchrotron_beamline | 08ID-1 |
Temperature [K] _diffrn.ambient_temp | 100 |
Detector technology _diffrn_detector.detector | PIXEL |
Collection date _diffrn_detector.pdbx_collection_date | 2017-09-17 |
Detector _diffrn_detector.type | DECTRIS PILATUS3 6M |
Wavelength(s) [Å] _diffrn_source.pdbx_wavelength_list | 0.97949 |
| Software | |
Data reduction _software.classification | XDS |
Data scaling _software.classification | Aimless (0.5.32) |
Phasing _software.classification | REFMAC |
Refinement _software.classification | REFMAC (5.8.0158) |
| General information | |
Spacegroup name _symmetry.space_group_name_H-M | P 1 |
Unit cell parameters _cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma} | 37.013 40.198 105.158 84.50 85.48 62.71 |
Wavelength _diffrn_radiation_wavelength.wavelength | 0.97949 Å |
| Data quality metrics | Overall | InnerShell | OuterShell |
|---|---|---|---|
Low resolution limit [Å] _reflns.d_resolution_low _reflns_shell.d_res_low | 35.640 | 35.640 | 2.050 |
High resolution limit [Å] _reflns.d_resolution_high _reflns_shell.d_res_high | 2.000 | 8.930 | 2.000 |
Rmerge _reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs | 0.040 | 0.024 | 0.760 |
Rmeas _reflns.pdbx_Rrim_I_all _reflns_shell.pdbx_Rrim_I_all | 0.054 | 0.031 | 1.032 |
Rpim _reflns.pdbx_Rpim_I_all _reflns_shell.pdbx_Rpim_I_all | 0.037 | 0.021 | 0.694 |
Total number of observations _reflns.pdbx_number_measured_all _reflns_shell.number_measured_all | 66586 | 769 | 3666 |
Total number unique _reflns.number_obs _reflns_shell.number_unique_obs | 34483 | 396 | 2199 |
<I/σ(I)> _reflns.pdbx_netI_over_sigmaI _reflns_shell.pdbx_netI_over_sigmaI_obs | 10.00 | 31.30 | 0.90 |
Completeness [%] _reflns.percent_possible_obs _reflns_shell.percent_possible_all | 94.8 | 96.6 | 81.4 |
Multiplicity _reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy | 1.9 | 1.9 | 1.7 |
CC(1/2) _reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half | 0.998 | 0.998 | 0.465 |
| Refinement | |
|---|---|
PDB entry ID _entry.id | 6C1V |
Deposition date _pdbx_database_status.recvd_initial_deposition_date | 2018-01-05 |
Resolution _refine.ls_d_res_low _refine.ls_d_res_high | 34.8 - 2.300 Å |
Rwork/Rfree _refine.ls_R_factor_R_work _refine.ls_R_factor_R_free | 0.2327 / 0.2677 |
Structure solution method _refine.pdbx_method_to_determine_struct | FOURIER SYNTHESIS |
Starting model _refine.pdbx_starting_model | rigid body refinement (refmac5/dimple) of a currently unpublished, isomorphous structure of a similar MBD2-DNA complex against current data. |