| 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 | CCD |
Collection date _diffrn_detector.pdbx_collection_date | 2015-01-30 |
Detector _diffrn_detector.type | MARMOSAIC 300 mm CCD |
Wavelength(s) [Å] _diffrn_source.pdbx_wavelength_list | 0.97957 |
| Software | |
Data reduction #1 _software.classification | XDS |
Data reduction #2 _software.classification | xia2 |
Data scaling _software.classification | Aimless (0.5.27) |
Phasing _software.classification | PHASER |
Refinement _software.classification | REFMAC (5.8.0155) |
| General information | |
Spacegroup name _symmetry.space_group_name_H-M | H 3 |
Unit cell parameters _cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma} | 210.75 210.75 67.20 90.0 90.0 120.0 |
Wavelength _diffrn_radiation_wavelength.wavelength | 0.97957 Å |
| Data quality metrics | Overall | InnerShell | OuterShell |
|---|---|---|---|
Low resolution limit [Å] _reflns.d_resolution_low _reflns_shell.d_res_low | 63.060 | 63.060 | 2.670 |
High resolution limit [Å] _reflns.d_resolution_high _reflns_shell.d_res_high | 2.600 | 11.630 | 2.600 |
Rmerge _reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs | 0.099 | 0.052 | 0.997 |
Rmeas _reflns.pdbx_Rrim_I_all _reflns_shell.pdbx_Rrim_I_all | 0.109 | 0.057 | 1.095 |
Rpim _reflns.pdbx_Rpim_I_all _reflns_shell.pdbx_Rpim_I_all | 0.045 | 0.024 | 0.452 |
Total number of observations _reflns.pdbx_number_measured_all _reflns_shell.number_measured_all | 200420 | 2090 | 14724 |
Total number unique _reflns.number_obs _reflns_shell.number_unique_obs | 34195 | 374 | 2515 |
<I/σ(I)> _reflns.pdbx_netI_over_sigmaI _reflns_shell.pdbx_netI_over_sigmaI_obs | 14.80 | 41.70 | 1.90 |
Completeness [%] _reflns.percent_possible_obs _reflns_shell.percent_possible_all | 100.0 | 98.9 | 100.0 |
Multiplicity _reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy | 5.9 | 5.6 | 5.9 |
CC(1/2) _reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half | 0.997 | 0.996 | 0.658 |
| Refinement | |
|---|---|
PDB entry ID _entry.id | 6V2H |
Deposition date _pdbx_database_status.recvd_initial_deposition_date | 2019-11-22 |
Resolution _refine.ls_d_res_low _refine.ls_d_res_high | 63.1 - 2.600 Å |
Rwork/Rfree _refine.ls_R_factor_R_work _refine.ls_R_factor_R_free | 0.2173 / 0.2366 |
Structure solution method _refine.pdbx_method_to_determine_struct | MOLECULAR REPLACEMENT |
Starting model (for MR) _refine.pdbx_starting_model | an early version of PDB entry 6V41 (CDY1 in complex with a histone peptide) |