| 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 | DIAMOND BEAMLINE I03 |
Synchrotron site _diffrn_source.pdbx_synchrotron_site | Diamond |
Beamline _diffrn_source.pdbx_synchrotron_beamline | I03 |
Temperature [K] _diffrn.ambient_temp | 100 |
Detector technology _diffrn_detector.detector | PIXEL |
Collection date _diffrn_detector.pdbx_collection_date | 2020-02-10 |
Detector _diffrn_detector.type | DECTRIS EIGER2 X 16M |
Wavelength(s) [Å] _diffrn_source.pdbx_wavelength_list | 0.987 |
| Software | |
Data reduction _software.classification | DIALS (V1-9-2) |
Data scaling _software.classification | xia2 (7.0.078) |
Phasing _software.classification | PHASER (1.17.1_3660) |
Model building _software.classification | Coot (8,9, Wincoot) |
Refinement _software.classification | PHENIX (1.17.1_3660) |
| General information | |
Spacegroup name _symmetry.space_group_name_H-M | I 2 2 2 |
Unit cell parameters _cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma} | 95.528 99.359 153.728 90.0 90.0 90.0 |
Wavelength _diffrn_radiation_wavelength.wavelength | 0.98700 Å |
| Data quality metrics | Overall | OuterShell |
|---|---|---|
Low resolution limit [Å] _reflns.d_resolution_low _reflns_shell.d_res_low | 68.900 | 1.730 |
High resolution limit [Å] _reflns.d_resolution_high _reflns_shell.d_res_high | 1.700 | 1.700 |
| Rmerge | - | - |
| Rmeas | - | - |
| Rpim | - | - |
| Total number of observations | - | - |
Total number unique _reflns.number_obs _reflns_shell.number_unique_obs | 79520 | 3622 |
<I/σ(I)> _reflns.pdbx_netI_over_sigmaI _reflns_shell.meanI_over_sigI_obs | 20.06 | 3.40 |
Completeness [%] _reflns.percent_possible_obs _reflns_shell.percent_possible_all | 98.9 | 89.4 |
Multiplicity _reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy | 12.4 | 7.6 |
CC(1/2) _reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half | 0.999 | 0.898 |
| Refinement | |
|---|---|
PDB entry ID _entry.id | 9GPG |
Deposition date _pdbx_database_status.recvd_initial_deposition_date | 2024-09-07 |
Resolution _refine.ls_d_res_low _refine.ls_d_res_high | 51.3 - 1.700 Å |
Rwork/Rfree _refine.ls_R_factor_R_work _refine.ls_R_factor_R_free | 0.1660 / 0.1831 |
Structure solution method _refine.pdbx_method_to_determine_struct | MOLECULAR REPLACEMENT |
Starting model (for MR) _refine.pdbx_starting_model | Native ManDH5 |