8KD0
Crystal structure of SAR11_0769 from 'Candidatus Pelagibacter ubique' HTCC1062 bound to a co-purified ligand, beta-galactopyranose
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SPRING-8 BEAMLINE BL32XU |
Synchrotron site | SPring-8 |
Beamline | BL32XU |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2023-06-09 |
Detector | DECTRIS EIGER X 9M |
Wavelength(s) | 1.0 |
Spacegroup name | P 32 2 1 |
Unit cell lengths | 43.879, 43.879, 328.555 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 38.029 - 1.675 |
Rwork | 0.194 |
R-free | 0.22880 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 8hqq |
RMSD bond length | 0.007 |
RMSD bond angle | 1.368 |
Data reduction software | XDS (Jun 30, 2023) |
Data scaling software | XDS (Jun 30, 2023) |
Phasing software | MOLREP (11.9.02) |
Refinement software | REFMAC (5.8.0405) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 46.936 | 1.780 |
High resolution limit [Å] | 1.670 | 1.670 |
Rmerge | 0.135 | 1.608 |
Rmeas | 0.141 | 1.683 |
Number of reflections | 43960 | 6771 |
<I/σ(I)> | 11.08 | 1.05 |
Completeness [%] | 99.6 | 97.3 |
Redundancy | 12.2 | 11.37 |
CC(1/2) | 0.997 | 0.864 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION | 6.5 | 293 | 20% (v/v) 2-propanol, 0.1 M MES pH 6.5, 23% (w/v) PEG 1500. 1.2 uL protein + 1.2 uL precipitant. |