4F36
Crystal structure of Nucleoside diphosphate kinase B from Trypanosoma brucei, apo form
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRL BEAMLINE BL7-1 |
Synchrotron site | SSRL |
Beamline | BL7-1 |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2012-04-26 |
Detector | ADSC QUANTUM 315r |
Wavelength(s) | 1.0331710 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 52.460, 123.670, 145.360 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 50.000 - 2.300 |
R-factor | 0.2 |
Rwork | 0.198 |
R-free | 0.23500 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3r9l |
RMSD bond length | 0.014 |
RMSD bond angle | 1.411 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | REFMAC (5.6.0117) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 2.360 | |
High resolution limit [Å] | 2.300 | 10.280 | 2.300 |
Rmerge | 0.077 | 0.052 | 0.486 |
Number of reflections | 42511 | 521 | 2857 |
<I/σ(I)> | 12.47 | 28.5 | 2.3 |
Completeness [%] | 98.8 | 92.5 | 91.3 |
Redundancy | 4.3 | 3.11 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 290 | EBS internal tracking number 233837B2: JCSG B2, protein: 20.2 mg/mL TrbrA.00438.a.B1 PS01459 in 25 mM HEPES, pH 7.0, 500 mM sodium chloride, 2 mM DTT, 0.025% sodium azide, 5% glycerol, crystallant: 20% PEG3350, 200 mM sodium isothiocyanate, VAPOR DIFFUSION, SITTING DROP, temperature 290K |