4EK2
The structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to deoxyadenosine monophosphate
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU FR-E+ SUPERBRIGHT |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2012-02-27 |
Detector | RIGAKU SATURN 944 |
Wavelength(s) | 1.5418 |
Spacegroup name | P 41 2 2 |
Unit cell lengths | 90.680, 90.680, 90.430 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 40.553 - 2.000 |
R-factor | 0.1916 |
Rwork | 0.190 |
R-free | 0.22820 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4dut |
RMSD bond length | 0.013 |
RMSD bond angle | 1.332 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | REFMAC |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 40.553 | 40.553 | 2.050 |
High resolution limit [Å] | 2.000 | 8.940 | 2.000 |
Rmerge | 0.066 | 0.018 | 0.219 |
Number of reflections | 25415 | 359 | 1593 |
<I/σ(I)> | 30.21 | 91.09 | 7.95 |
Completeness [%] | 97.2 | 96.5 | 84.4 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 289 | ButhA.00438.a.A1 PS01186 at 42.64 mg/mL in 1.5 M ammonium sulfate, 0.1 M Bis-Tris propane, pH 7.0, 10 mM dAMP, cryoprotectant: 15% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K |