1WKK
Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with GDP
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SPRING-8 BEAMLINE BL38B1 |
Synchrotron site | SPring-8 |
Beamline | BL38B1 |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2003-12-02 |
Detector | RIGAKU JUPITER 210 |
Wavelength(s) | 1.0 |
Spacegroup name | P 63 2 2 |
Unit cell lengths | 123.830, 123.830, 104.302 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 50.000 - 2.700 |
Rwork | 0.201 |
R-free | 0.24000 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1wkj |
RMSD bond length | 0.006 |
RMSD bond angle | 1.200 |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | AMoRE |
Refinement software | CNS (1.1) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 2.800 |
High resolution limit [Å] | 2.700 | 2.700 |
Rmerge | 0.099 | 0.251 |
Number of reflections | 161023 | |
<I/σ(I)> | 40.2 | 16.2 |
Completeness [%] | 99.7 | 100 |
Redundancy | 12.1 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.4 | 293 | 13% PEG4000, 0.09M Ammonium Acetate, 15% Glycerol, 0.1M Sodium Citrate, 0.001M GTP, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |