4HR2
Structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to ADP
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU FR-E+ SUPERBRIGHT |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2012-09-09 |
Detector | RIGAKU SATURN 944+ |
Wavelength(s) | 1.5418 |
Spacegroup name | P 41 2 2 |
Unit cell lengths | 91.240, 91.240, 90.190 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 40.427 - 1.950 |
R-factor | 0.2092 |
Rwork | 0.208 |
R-free | 0.24040 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4ek2 |
RMSD bond length | 0.009 |
RMSD bond angle | 1.413 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER (2.5.1) |
Refinement software | REFMAC |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 40.427 | 2.000 | |
High resolution limit [Å] | 1.950 | 8.720 | 1.950 |
Rmerge | 0.062 | 0.019 | 0.442 |
Number of reflections | 27811 | 363 | 1957 |
<I/σ(I)> | 21.37 | 69.07 | 2.76 |
Completeness [%] | 97.9 | 90.8 | 95.3 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 298 | ButhA.00438.a.A1 PS01186 at 42.64 mg/mL, 1.5 M ammonium sulfate, 0.1 M Bis-Tris propane, pH 7.0, cryoprotectant: 15% ethylene glycol, 1mM ADP, VAPOR DIFFUSION, SITTING DROP, temperature 298K |