5U2I
Crystal structure of a nucleoside diphosphate kinase from Naegleria fowleri
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 | 2016-10-12 |
Detector | MARMOSAIC 225 mm CCD |
Wavelength(s) | 0.97872 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 67.900, 110.380, 68.140 |
Unit cell angles | 90.00, 118.55, 90.00 |
Refinement procedure
Resolution | 40.575 - 1.400 |
R-factor | 0.141 |
Rwork | 0.141 |
R-free | 0.16890 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3vvt |
RMSD bond length | 0.010 |
RMSD bond angle | 1.110 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | MoRDa |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 40.592 | 1.440 | |
High resolution limit [Å] | 1.400 | 6.260 | 1.400 |
Rmerge | 0.113 | 0.090 | 0.405 |
Number of reflections | 172534 | ||
<I/σ(I)> | 9.08 | 15.34 | 3.37 |
Completeness [%] | 99.6 | 98.4 | 99.8 |
Redundancy | 4.16 | ||
CC(1/2) | 0.988 | 0.980 | 0.864 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 290 | Rigaku Reagents MCSG1 screen g10: 0.1M Mg Formate, 15% PEG3350; NafoA.00438.a.B1.PS38003 at 17.9 mg/mL. Tray 283886 g10, puck fhx0-10; cryoprotected in 20% ethylene glycol |