6MJK
Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri in complex with deoxyuridine
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-F |
Synchrotron site | APS |
Beamline | 21-ID-F |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2017-03-15 |
Detector | RAYONIX MX-300 |
Wavelength(s) | 0.97856 |
Spacegroup name | P 21 3 |
Unit cell lengths | 74.230, 74.230, 74.230 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 33.197 - 1.450 |
R-factor | 0.1369 |
Rwork | 0.134 |
R-free | 0.16980 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4oop |
RMSD bond length | 0.005 |
RMSD bond angle | 0.783 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX ((1.14rc2_3191: ???)) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 33.197 | 33.197 | 1.490 |
High resolution limit [Å] | 1.450 | 6.480 | 1.450 |
Rmerge | 0.039 | 0.020 | 0.497 |
Rmeas | 0.041 | 0.021 | 0.512 |
Total number of observations | 416266 | ||
Number of reflections | 24498 | 321 | 1801 |
<I/σ(I)> | 46.35 | 116 | 5.79 |
Completeness [%] | 100.0 | 99.1 | 100 |
Redundancy | 16.992 | 13.003 | 16.977 |
CC(1/2) | 1.000 | 1.000 | 0.959 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 290 | JCSG+ C6: 40% PEG 300 + 100mM Sodium phosphate dibasic / sodium citrate pH 4.2:cryo:direct. PW37974 22.5mg/mL, 0.4+0.4, 6 mM dUTP + 6 mM MgCl2 puck xbp1-8, tray286723C6 |