3R9L
Crystal structure of nucleoside diphosphate kinase from Giardia lamblia featuring a disordered dinucleotide binding site
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 | CCD |
Collection date | 2011-03-04 |
Detector | ADSC QUANTUM 315r |
Wavelength(s) | 0.97946 |
Spacegroup name | P 63 2 2 |
Unit cell lengths | 116.960, 116.960, 62.690 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 39.400 - 2.650 |
R-factor | 0.2359 |
Rwork | 0.234 |
R-free | 0.26630 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1npk |
RMSD bond length | 0.012 |
RMSD bond angle | 1.278 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER (2.1.4) |
Refinement software | REFMAC |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 2.720 | |
High resolution limit [Å] | 2.650 | 11.850 | 2.650 |
Rmerge | 0.049 | 0.011 | 0.526 |
Number of reflections | 7665 | 102 | 567 |
<I/σ(I)> | 26.02 | 75.2 | 3.26 |
Completeness [%] | 98.8 | 85 | 100 |
Redundancy | 5.6 | 6 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.9 | 289 | GilaA.00438.a.A1 PW27083 at 24.97 mg/mL in 25 mM Hepes pH 7.0, 0.5 M NaCl, 5% glycerol, 2 mM DTT, 0.025% azide against CSHT C11 focus screen 0.1 M Hepes pH 7.0, 0.9 M Na phosphate, 0.9 M K phosphate with 25% ethylene glycol as cryo-protectant, crystal tracking ID 216300h9, VAPOR DIFFUSION, SITTING DROP, temperature 289K |