6M5O
Co-crystal structure of human serine hydroxymethyltransferase 2 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SPRING-8 BEAMLINE BL26B2 |
Synchrotron site | SPring-8 |
Beamline | BL26B2 |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2019-05-28 |
Detector | RAYONIX MX-225 |
Wavelength(s) | 1.0 |
Spacegroup name | P 65 2 2 |
Unit cell lengths | 159.840, 159.840, 211.210 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 49.356 - 2.300 |
R-factor | 0.203792694894 |
Rwork | 0.201 |
R-free | 0.25587 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4pvf |
RMSD bond length | 0.007 |
RMSD bond angle | 0.962 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.11) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 49.356 | 4.950 | 2.380 |
High resolution limit [Å] | 2.300 | 3.930 | 2.300 |
Rmerge | 0.316 | 0.115 | 1.878 |
Rmeas | 0.324 | 0.118 | 1.921 |
Number of reflections | 70999 | 159076 | 157463 |
<I/σ(I)> | 12.4 | 28.2 | 2.3 |
Completeness [%] | 100.0 | 100 | 100 |
Redundancy | 22.25 | 22.06 | 22.48 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 0.1 M Tris hydrochloride pH 8.5, 8% (w/v) polyethylene glycol 8000 |