Experiment | |
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Method _exptl.method | X-RAY DIFFRACTION The method used in the experiment. |
Experimental protocol _diffrn_radiation.pdbx_diffrn_protocol | SINGLE WAVELENGTH SINGLE WAVELENGTH, LAUE, or MAD. |
Source type _diffrn_source.source | SYNCHROTRON The general class of the radiation source. |
Source details _diffrn_source.type | SPRING-8 BEAMLINE BL45XU The make, model or name of the source of radiation. |
Synchrotron site _diffrn_source.pdbx_synchrotron_site | SPring-8 Synchrotron site. |
Beamline _diffrn_source.pdbx_synchrotron_beamline | BL45XU Synchrotron beamline. |
Temperature [K] _diffrn.ambient_temp | 100 The mean temperature in kelvins at which the intensities were |
Detector technology _diffrn_detector.detector | PIXEL The general class of the radiation detector. |
Collection date _diffrn_detector.pdbx_collection_date | 2021-10-23 The date of data collection. |
Detector _diffrn_detector.type | DECTRIS PILATUS3 6M The make, model or name of the detector device used. |
Wavelength(s) [Å] _diffrn_source.pdbx_wavelength_list | 1.00000 Comma separated list of wavelengths or wavelength range. |
Software | |
Data processing _software.classification | autoPROC The classification of the program according to its |
Data reduction _software.classification | XDS (Jan 31, 2020) The classification of the program according to its |
Data scaling #1 _software.classification | Aimless (0.7.7) The classification of the program according to its |
Data scaling #2 _software.classification | STARANISO (2.3.63) The classification of the program according to its |
Phasing _software.classification | PHASER The classification of the program according to its |
Refinement #1 _software.classification | PHENIX (1.20.1) The classification of the program according to its |
Refinement #2 _software.classification | BUSTER (2.11.8 (3-FEB-2022)) The classification of the program according to its |
General information | |
Spacegroup name _symmetry.space_group_name_H-M | C 1 2 1 Hermann-Mauguin space-group symbol. Note that the |
Unit cell parameters _cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma} | 84.890 Unit-cell length a corresponding to the structure reported in 62.298 Unit-cell length b corresponding to the structure reported in 81.636 Unit-cell length c corresponding to the structure reported in 90.00 Unit-cell angle alpha of the reported structure in degrees. 105.55 Unit-cell angle beta of the reported structure in degrees. 90.00 Unit-cell angle gamma of the reported structure in degrees. |
Wavelength _diffrn_radiation_wavelength.wavelength | 1.00000 ÅThe radiation wavelength in angstroms. |
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] | ||
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1.186 ÅAnisotropic diffraction limit along principal axis 1 (of | 0.8536 Principal axis 1 (X component) of ellipsoid fitted to the | 0.0000 Principal axis 1 (Y component) of ellipsoid fitted to the | 0.5211 Principal axis 1 (Z component) of ellipsoid fitted to the |
1.300 ÅAnisotropic diffraction limit along principal axis 2 (of | 0.0000 Principal axis 2 (X component) of ellipsoid fitted to the | 1.0000 Principal axis 2 (Y component) of ellipsoid fitted to the | 0.0000 Principal axis 2 (Z component) of ellipsoid fitted to the |
1.293 ÅAnisotropic diffraction limit along principal axis 3 (of | -0.5211 Principal axis 3 (X component) of ellipsoid fitted to the | 0.0000 Principal axis 3 (Y component) of ellipsoid fitted to the | 0.8536 Principal axis 3 (Z component) of ellipsoid fitted to the |
Data quality metrics | Overall | InnerShell | OuterShell |
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Low resolution limit [Å] _reflns.d_resolution_low _reflns_shell.d_res_low | 49.558 The largest value in angstroms for the interplanar spacings | 49.558 The highest value in angstroms for the interplanar spacings | 1.289 The highest value in angstroms for the interplanar spacings |
High resolution limit [Å] _reflns.d_resolution_high _reflns_shell.d_res_high | 1.186 The smallest value in angstroms for the interplanar spacings | 3.508 The smallest value in angstroms for the interplanar spacings | 1.186 The smallest value in angstroms for the interplanar spacings |
Rmerge _reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs | 0.036 The R value for merging intensities satisfying the observed | 0.025 The value of Rmerge(I) for reflections classified as 'observed' | 0.967 The value of Rmerge(I) for reflections classified as 'observed' |
Rmeas _reflns.pdbx_Rrim_I_all _reflns_shell.pdbx_Rrim_I_all | 0.041 The redundancy-independent merging R factor value Rrim, | 0.028 The redundancy-independent merging R factor value Rrim, | 1.069 The redundancy-independent merging R factor value Rrim, |
Rpim _reflns.pdbx_Rpim_I_all _reflns_shell.pdbx_Rpim_I_all | 0.018 The precision-indicating merging R factor value Rpim, | 0.013 The precision-indicating merging R factor value Rpim, | 0.452 The precision-indicating merging R factor value Rpim, |
Total number of observations _reflns.pdbx_number_measured_all _reflns_shell.number_measured_all | 495020 Total number of measured reflections. | 23784 The total number of reflections measured for this | 28790 The total number of reflections measured for this |
Total number unique _reflns.number_obs _reflns_shell.number_unique_all | 104460 The number of reflections in the REFLN list (not the DIFFRN_REFLN | 5223 The total number of measured reflections which are symmetry- | 5226 The total number of measured reflections which are symmetry- |
<I/σ(I)> _reflns.pdbx_netI_over_sigmaI _reflns_shell.meanI_over_sigI_obs | 11.42 The mean of the ratio of the intensities to their | 28.89 The ratio of the mean of the intensities of the reflections | 1.44 The ratio of the mean of the intensities of the reflections |
Completeness (spherical) [%] _reflns.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_spherical | 78.8 Completeness (as a percentage) of symmetry-unique data | 99.4 Completeness (as a percentage) of symmetry-unique data | 17.8 Completeness (as a percentage) of symmetry-unique data |
Completeness (ellipsoidal) [%] _reflns.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_ellipsoidal | 93.5 Completeness (as a percentage) of symmetry-unique data | 99.4 Completeness (as a percentage) of symmetry-unique data | 57.2 Completeness (as a percentage) of symmetry-unique data |
Multiplicity _reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy | 4.7 Overall redundancy for this data set. | 4.5 Redundancy for the current shell. | 5.5 Redundancy for the current shell. |
CC(1/2) _reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half | 0.999 The Pearson's correlation coefficient expressed as a decimal value | 0.999 The Pearson's correlation coefficient expressed as a decimal value | 0.610 The Pearson's correlation coefficient expressed as a decimal value |
Anomalous completeness (spherical) _reflns.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous | 76.8 Completeness (as a percentage) of symmetry-unique | 98.1 Completeness (as a percentage) of symmetry-unique | 17.6 Completeness (as a percentage) of symmetry-unique |
Anomalous completeness (ellipsoidal) _reflns.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous | 91.3 Completeness (as a percentage) of symmetry-unique | 98.1 Completeness (as a percentage) of symmetry-unique | 57.1 Completeness (as a percentage) of symmetry-unique |
Anomalous multiplicity _reflns.pdbx_redundancy_anomalous _reflns_shell.pdbx_redundancy_anomalous | 2.4 The overall redundancy of anomalous difference data | 2.4 The redundancy of anomalous difference data within the | 2.8 The redundancy of anomalous difference data within the |
CC(ano) _reflns.pdbx_CC_half_anomalous _reflns_shell.pdbx_CC_half_anomalous | -0.117 The overall correlation coefficient between two randomly | -0.126 The correlation coefficient within the spherical shell | 0.011 The correlation coefficient within the spherical shell |
|DANO|/σ(DANO) _reflns.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous | 0.615 The overall mean ratio of absolute anomalous intensity | 0.416 The mean ratio of absolute anomalous intensity | 0.647 The mean ratio of absolute anomalous intensity |
Refinement | |
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PDB entry ID _entry.id | 8GV1 |
Deposition date _pdbx_database_status.recvd_initial_deposition_date | 2022-09-14 |
Resolution _refine.ls_d_res_low _refine.ls_d_res_high | 49.6 - 1.186 Å |
Rwork/Rfree _refine.ls_R_factor_R_work _refine.ls_R_factor_R_free | 0.2059 / 0.2265 |
Structure solution method _refine.pdbx_method_to_determine_struct | MOLECULAR REPLACEMENT |
Starting model (for MR) _refine.pdbx_starting_model | 5DK3 |