| 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 | ESRF BEAMLINE ID29 |
Synchrotron site _diffrn_source.pdbx_synchrotron_site | ESRF |
Beamline _diffrn_source.pdbx_synchrotron_beamline | ID29 |
Temperature [K] _diffrn.ambient_temp | 100 |
Detector technology _diffrn_detector.detector | PIXEL |
Collection date _diffrn_detector.pdbx_collection_date | 2018-11-22 |
Detector _diffrn_detector.type | DECTRIS PILATUS 6M |
Wavelength(s) [Å] _diffrn_source.pdbx_wavelength_list | 1.072270 |
| Software | |
Data reduction _software.classification | XDS (January 26, 2018) |
Data scaling #1 _software.classification | STARANISO (2.2.7 (8-Dec-2018)) |
Data scaling #2 _software.classification | Aimless (0.7.3) |
Phasing _software.classification | PHASER (2.7.17) |
Model building _software.classification | Coot (0.8.9.1) |
Refinement _software.classification | PHENIX (1.14rc1_3177) |
| General information | |
Spacegroup name _symmetry.space_group_name_H-M | P 4 21 2 |
Unit cell parameters _cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma} | 122.107 122.107 133.697 90.0 90.0 90.0 |
Wavelength _diffrn_radiation_wavelength.wavelength | 1.07227 Å |
| Data quality metrics | Overall | OuterShell |
|---|---|---|
Low resolution limit [Å] _reflns.d_resolution_low _reflns_shell.d_res_low | 45.081 | 2.994 |
High resolution limit [Å] _reflns.d_resolution_high _reflns_shell.d_res_high | 2.748 | 2.748 |
Rmerge _reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs | 0.310 | 1.668 |
Rmeas _reflns.pdbx_Rrim_I_all _reflns_shell.pdbx_Rrim_I_all | 0.347 | 1.739 |
Rpim _reflns.pdbx_Rpim_I_all _reflns_shell.pdbx_Rpim_I_all | 0.090 | 0.486 |
| Total number of observations | - | - |
Total number unique _reflns.number_obs _reflns_shell.number_unique_obs | 14539 | 902 |
<I/σ(I)> _reflns.pdbx_netI_over_sigmaI _reflns_shell.meanI_over_sigI_obs | 7.80 | 1.80 |
Completeness [%] _reflns.percent_possible_obs _reflns_shell.percent_possible_all | 53.8 | 15.0 |
Multiplicity _reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy | 12.6 | 12.5 |
CC(1/2) _reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half | 0.996 | 0.627 |
| Refinement | |
|---|---|
PDB entry ID _entry.id | 6RHW |
Deposition date _pdbx_database_status.recvd_initial_deposition_date | 2019-04-23 |
Resolution _refine.ls_d_res_low _refine.ls_d_res_high | 45.1 - 2.750 Å |
Rwork/Rfree _refine.ls_R_factor_R_work _refine.ls_R_factor_R_free | 0.2393 / 0.2812 |
Structure solution method _refine.pdbx_method_to_determine_struct | MOLECULAR REPLACEMENT |
Starting model (for MR) _refine.pdbx_starting_model | LukGH dimer from the structure of its complex with mouse CD11b I-domain (CD11b-I) and the modified huCD11b-I domain (PDB code 1IDO) lacking the C-terminal alpha-helix (residues 303-315) |