7LJU
Porcine Dihydropyrimidine Dehydrogenase (DPD) crosslinked with 5-Ethynyluracil (5EU)
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 | 2020-12-09 |
Detector | DECTRIS EIGER2 X 9M |
Wavelength(s) | 1.1272 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 82.060, 158.940, 163.210 |
Unit cell angles | 90.00, 96.03, 90.00 |
Refinement procedure
Resolution | 40.590 - 1.870 |
R-factor | 0.1739 |
Rwork | 0.172 |
R-free | 0.21090 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1h7x |
Data reduction software | xia2 |
Data scaling software | xia2 |
Phasing software | PHASER |
Refinement software | PHENIX (1.19_4092) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 45.460 | 45.460 | 1.920 |
High resolution limit [Å] | 1.870 | 8.360 | 1.870 |
Rmerge | 0.215 | 0.069 | 1.066 |
Rpim | 0.117 | 0.037 | 0.668 |
Number of reflections | 336013 | 3888 | 23294 |
<I/σ(I)> | 6.3 | 19 | 1.1 |
Completeness [%] | 98.3 | 98.6 | 92.4 |
Redundancy | 4.1 | 4.1 | 3.4 |
CC(1/2) | 0.989 | 0.993 | 0.520 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | DPD was crystallized by the vapor diffusion, hanging drop method by mixing 3 uL of 39 uM DPD in 25 mM HEPES, 2 mM DTT, 10% glycerol, pH 7.5 with 3 uL of well solution containing 100 mM NaCl, 2 mM DTT, 18% PEG 6000, pH 4.7. Rectangular hexahedron crystals grew in ~16-20 hours to a size of approximately 50 x 200 x 20 um. The crystals were soaked for 2 hours in 25 mM HEPES, 100 mM NaCl, 2 mM DTT, 100 uM NADPH, 100 uM 5EU, 20% PEG 6000, 20% PEG 400, pH 7.5. The whole procedure has been done anaerobically in the glove box. |