6PLG
Crystal structure of human PHGDH complexed with Compound 15
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE ID30B |
Synchrotron site | ESRF |
Beamline | ID30B |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-06-21 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.97625 |
Spacegroup name | P 1 |
Unit cell lengths | 44.649, 112.699, 137.840 |
Unit cell angles | 105.98, 96.20, 101.42 |
Refinement procedure
Resolution | 45.420 - 2.930 |
R-factor | 0.2761 |
Rwork | 0.274 |
R-free | 0.31480 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.008 |
RMSD bond angle | 1.766 |
Data reduction software | HKL-2000 |
Data scaling software | SCALEPACK |
Refinement software | REFMAC (5.8.0253) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 3.030 |
High resolution limit [Å] | 2.930 | 6.310 | 2.930 |
Rmerge | 0.099 | 0.032 | 0.577 |
Rmeas | 0.140 | 0.046 | 0.816 |
Rpim | 0.099 | 0.032 | 0.577 |
Total number of observations | 83204 | ||
Number of reflections | 49500 | 5013 | 4939 |
<I/σ(I)> | 6.8 | ||
Completeness [%] | 93.3 | 94.7 | 93.5 |
Redundancy | 1.7 | 1.7 | 1.7 |
CC(1/2) | 0.997 | 0.750 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 297 | 27% PEG mme 5000, 180 mM ammonium sulfate, 90 mM MES pH 6.5, 2% glycerol, and 20 mM DL-malic acid pH 7.0 |