6PLF
Crystal structure of human PHGDH complexed with Compound 1
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-D |
Synchrotron site | APS |
Beamline | 21-ID-D |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2016-11-11 |
Detector | DECTRIS EIGER X 9M |
Wavelength(s) | 1.07822 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 43.202, 126.192, 59.504 |
Unit cell angles | 90.00, 99.76, 90.00 |
Refinement procedure
Resolution | 40.370 - 1.700 |
R-factor | 0.1864 |
Rwork | 0.184 |
R-free | 0.22330 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.010 |
RMSD bond angle | 1.700 |
Data reduction software | HKL-2000 |
Data scaling software | SCALEPACK |
Refinement software | REFMAC (5.8.0238) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.760 |
High resolution limit [Å] | 1.700 | 3.660 | 1.700 |
Rmerge | 0.060 | 0.040 | 0.568 |
Rmeas | 0.072 | 0.048 | 0.692 |
Rpim | 0.039 | 0.025 | 0.390 |
Total number of observations | 209488 | ||
Number of reflections | 66230 | 6885 | 6538 |
<I/σ(I)> | 14.6 | ||
Completeness [%] | 96.0 | 98.4 | 95 |
Redundancy | 3.2 | 3.5 | 2.9 |
CC(1/2) | 0.996 | 0.766 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 297 | 0.1 M Bis-Tris pH 5.5 and a range of PEG 3350 (24% to 29%), using micro-seeding |