| 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 | PHOTON FACTORY BEAMLINE BL-1A |
Synchrotron site _diffrn_source.pdbx_synchrotron_site | Photon Factory |
Beamline _diffrn_source.pdbx_synchrotron_beamline | BL-1A |
Temperature [K] _diffrn.ambient_temp | 95 |
Detector technology _diffrn_detector.detector | PIXEL |
Collection date _diffrn_detector.pdbx_collection_date | 2024-03-18 |
Detector _diffrn_detector.type | DECTRIS EIGER X 4M |
Wavelength(s) [Å] _diffrn_source.pdbx_wavelength_list | 1.020000 |
| Software | |
Data processing _software.classification | autoPROC (1.1.7) |
Data reduction _software.classification | XDS (Jan 31, 2020) |
Data scaling #1 _software.classification | Aimless (0.7.15) |
Data scaling #2 _software.classification | STARANISO (2.3.94) |
Data scaling #3 _software.classification | pointless (1.12.16) |
Phasing _software.classification | PHASER |
Refinement _software.classification | BUSTER (2.11.8) |
| General information | |
Spacegroup name _symmetry.space_group_name_H-M | C 1 2 1 |
Unit cell parameters _cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma} | 126.642 76.410 48.222 90.00 105.44 90.00 |
Wavelength _diffrn_radiation_wavelength.wavelength | 1.02000 Å |
Diffraction limits _reflns.pdbx_aniso_diffraction_limit_{1,2,3} | Principal axes of ellipsoid fitted to diffraction cut-off surface _reflns.pdbx_aniso_diffraction_limit_axis_{1,2,3}_ortho[1..3] | ||
|---|---|---|---|
| 2.048 Å | 0.7343 | 0.0000 | 0.6788 |
| 1.708 Å | 0.0000 | 0.0000 | 0.0000 |
| 1.668 Å | 0.0000 | 0.0000 | 0.0000 |
| Criteria used in determination of diffraction limits: | ||
|---|---|---|
| local <I/sigmaI> | ≥ | 1.20 |
| Data quality metrics | Overall | InnerShell | OuterShell |
|---|---|---|---|
Low resolution limit [Å] _reflns.d_resolution_low _reflns_shell.d_res_low | 64.768 | 64.768 | 1.819 |
High resolution limit [Å] _reflns.d_resolution_high _reflns_shell.d_res_high | 1.699 | 5.066 | 1.699 |
Rmerge _reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs | 0.199 | 0.065 | 1.502 |
Rmeas _reflns.pdbx_Rrim_I_all _reflns_shell.pdbx_Rrim_I_all | 0.215 | 0.071 | 1.625 |
Rpim _reflns.pdbx_Rpim_I_all _reflns_shell.pdbx_Rpim_I_all | 0.081 | 0.027 | 0.618 |
Total number of observations _reflns.pdbx_number_measured_all _reflns_shell.number_measured_all | 268917 | 13910 | 13047 |
Total number unique _reflns.number_obs _reflns_shell.number_unique_all | 38151 | 1908 | 1908 |
<I/σ(I)> _reflns.pdbx_netI_over_sigmaI _reflns_shell.meanI_over_sigI_obs | 7.72 | 22.62 | 1.43 |
Completeness (spherical) [%] _reflns.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_spherical | 78.1 | 100.0 | 21.2 |
Completeness (ellipsoidal) [%] _reflns.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_ellipsoidal | 93.0 | 100.0 | 51.9 |
Multiplicity _reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy | 7.0 | 7.3 | 6.8 |
CC(1/2) _reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half | 0.990 | 0.959 | 0.555 |
Anomalous completeness (spherical) _reflns.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous | 77.7 | 99.9 | 21.3 |
Anomalous completeness (ellipsoidal) _reflns.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous | 92.6 | 99.9 | 51.9 |
Anomalous multiplicity _reflns.pdbx_redundancy_anomalous _reflns_shell.pdbx_redundancy_anomalous | 3.6 | 3.8 | 3.4 |
CC(ano) _reflns.pdbx_CC_half_anomalous _reflns_shell.pdbx_CC_half_anomalous | -0.061 | -0.197 | -0.001 |
|DANO|/σ(DANO) _reflns.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous | 0.744 | 0.759 | 0.701 |
| Refinement | |
|---|---|
PDB entry ID _entry.id | 9VD2 |
Deposition date _pdbx_database_status.recvd_initial_deposition_date | 2025-06-07 |
Resolution _refine.ls_d_res_low _refine.ls_d_res_high | 33.0 - 1.699 Å |
Rwork/Rfree _refine.ls_R_factor_R_work _refine.ls_R_factor_R_free | 0.1854 / 0.2118 |
Structure solution method _refine.pdbx_method_to_determine_struct | MOLECULAR REPLACEMENT |
Starting model (for MR) _refine.pdbx_starting_model | WARNING: no starting model (for MR) given |