8DKG
Structure of PYCR1 Thr171Met variant complexed with NADH
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 24-ID-E |
Synchrotron site | APS |
Beamline | 24-ID-E |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2022-03-28 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.97918 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 110.603, 179.929, 88.304 |
Unit cell angles | 90.00, 107.01, 90.00 |
Refinement procedure
Resolution | 55.380 - 1.850 |
R-factor | 0.1899 |
Rwork | 0.188 |
R-free | 0.21750 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6xp3 |
Data reduction software | XDS |
Data scaling software | Aimless (0.5.32) |
Phasing software | PHENIX (1.19.2) |
Refinement software | PHENIX (1.19.2) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 91.180 | 91.180 | 1.870 |
High resolution limit [Å] | 1.840 | 10.070 | 1.840 |
Rmerge | 0.128 | 0.036 | 1.918 |
Rmeas | 0.139 | 0.039 | 2.098 |
Rpim | 0.052 | 0.015 | 0.826 |
Total number of observations | 5811 | 31394 | |
Number of reflections | 275613 | 894 | 5414 |
<I/σ(I)> | 11.6 | 45.9 | 0.7 |
Completeness [%] | 98.5 | 99.2 | 76.7 |
Redundancy | 6.9 | 6.5 | 5.8 |
CC(1/2) | 0.998 | 0.999 | 0.435 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Reservoir contained 360 mM Li2SO4, 20% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 2 mM NADH and 5 mM N-formyl-L-proline. Crystal was soaked in cryobuffer containing 20% PEG 200 |