8GKY
Human mitochondrial serine hydroxymethyltransferase (SHMT2) Y105F in complex with PLP, glycine and AGF359 inhibitor
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ALS BEAMLINE 4.2.2 |
Synchrotron site | ALS |
Beamline | 4.2.2 |
Temperature [K] | 100 |
Detector technology | CMOS |
Collection date | 2021-12-08 |
Detector | RDI CMOS_8M |
Wavelength(s) | 1.000 |
Spacegroup name | P 65 2 2 |
Unit cell lengths | 157.971, 157.971, 206.460 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 48.515 - 2.770 |
R-factor | 0.2008 |
Rwork | 0.199 |
R-free | 0.24280 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.004 |
RMSD bond angle | 0.681 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.13-2998) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 48.520 | 2.880 |
High resolution limit [Å] | 2.770 | 2.770 |
Rmerge | 0.508 | 2.724 |
Rmeas | 0.530 | 2.846 |
Rpim | 0.149 | 0.811 |
Number of reflections | 39310 | 4350 |
<I/σ(I)> | 7.8 | 1 |
Completeness [%] | 100.0 | |
Redundancy | 12.5 | |
CC(1/2) | 0.985 | 0.377 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | BATCH MODE | 7.5 | 277 | 20 mM sodium phosphate pH 7.5, 100 mM NaCl, 0.2 mM EDTA, and 0.5 mM TCEP and PLP loaded His-SHMT2 concentrated to 0.01 to 0.02 mM |