| 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 | SLS BEAMLINE X06DA |
Synchrotron site _diffrn_source.pdbx_synchrotron_site | SLS |
Beamline _diffrn_source.pdbx_synchrotron_beamline | X06DA |
Temperature [K] _diffrn.ambient_temp | 100 |
Detector technology _diffrn_detector.detector | PIXEL |
Collection date _diffrn_detector.pdbx_collection_date | 2018-04-12 |
Detector _diffrn_detector.type | DECTRIS PILATUS 2M-F |
Wavelength(s) [Å] _diffrn_source.pdbx_wavelength_list | 1.00 |
| Software | |
Data reduction _software.classification | XDS (Wolfgang Kabsch; Wolfgang.Kabsch@mpimf-heidelberg.mpg.de) |
Data scaling _software.classification | Aimless (0.6.3; 01/02/18; Phil Evans) |
Phasing _software.classification | PHASER (Randy J. Read; cimr-phaser@lists.cam.ac.uk) |
Refinement _software.classification | PHENIX (1.14rc1_3177; Paul D. Adams; PDAdams@lbl.gov) |
| General information | |
Spacegroup name _symmetry.space_group_name_H-M | P 21 21 21 |
Unit cell parameters _cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma} | 48.271 90.531 120.717 90.0 90.0 90.0 |
Wavelength _diffrn_radiation_wavelength.wavelength | 1.00000 Å |
| Data quality metrics | Overall | InnerShell | OuterShell |
|---|---|---|---|
Low resolution limit [Å] _reflns.d_resolution_low _reflns_shell.d_res_low | 48.270 | 48.270 | 1.840 |
High resolution limit [Å] _reflns.d_resolution_high _reflns_shell.d_res_high | 1.800 | 9.000 | 1.800 |
Rmerge _reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs | 0.257 | 0.065 | 3.560 |
Rmeas _reflns.pdbx_Rrim_I_all _reflns_shell.pdbx_Rrim_I_all | 0.261 | 0.067 | 3.653 |
Rpim _reflns.pdbx_Rpim_I_all _reflns_shell.pdbx_Rpim_I_all | 0.046 | 0.012 | 0.815 |
| Total number of observations | - | - | - |
Total number unique _reflns.number_obs _reflns_shell.number_unique_obs | 49960 | 488 | 2885 |
<I/σ(I)> _reflns.pdbx_netI_over_sigmaI | 12.40 | - | - |
Completeness [%] _reflns.percent_possible_obs _reflns_shell.percent_possible_all | 99.9 | 99.6 | 98.6 |
Multiplicity _reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy | 32.7 | 29.9 | 19.8 |
CC(1/2) _reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half | 0.982 | 0.999 | 0.816 |
| Refinement | |
|---|---|
PDB entry ID _entry.id | 6YHN |
Deposition date _pdbx_database_status.recvd_initial_deposition_date | 2020-03-30 |
Resolution _refine.ls_d_res_low _refine.ls_d_res_high | 45.3 - 1.800 Å |
Rwork/Rfree _refine.ls_R_factor_R_work _refine.ls_R_factor_R_free | 0.1581 / 0.1910 |
Structure solution method _refine.pdbx_method_to_determine_struct | MOLECULAR REPLACEMENT |
Starting model (for MR) _refine.pdbx_starting_model | Corresponding fragment from the full-length toxin |