7N6S
Crystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia prowazekii str. Madrid E in complex with 2'-deoxyuridine 5'-monophoephate (dUMP)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ALS BEAMLINE 5.0.1 |
Synchrotron site | ALS |
Beamline | 5.0.1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-05-09 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.9774 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 50.720, 87.000, 183.340 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 45.830 - 1.750 |
R-factor | 0.1725 |
Rwork | 0.172 |
R-free | 0.20530 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7n56 apo structure |
RMSD bond length | 0.008 |
RMSD bond angle | 0.905 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.19 dev 4224) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.800 |
High resolution limit [Å] | 1.750 | 7.830 | 1.750 |
Rmerge | 0.036 | 0.015 | 0.485 |
Rmeas | 0.039 | 0.016 | 0.533 |
Number of reflections | 82624 | 1057 | 6008 |
<I/σ(I)> | 30.17 | 88.05 | 3.23 |
Completeness [%] | 99.8 | 99.4 | 99.9 |
Redundancy | 7.073 | 6.324 | 5.944 |
CC(1/2) | 1.000 | 1.000 | 0.881 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 287 | Anatrace / Calibre MCSG1 screen, condition H9: 100mM BisTris /HCl pH 5.5, 25% (w/V) PEG 3350: RiprA.10050.a.A1.PS00480 at 24mg/ml + 5mM dUMP / MgCl2: tray 320891 h9: cryo: 20% glycerol + compounds: puck bqq7-7 |