4HP8
Crystal structure of a putative 2-deoxy-d-gluconate 3-dehydrogenase from Agrobacterium Tumefaciens (target EFI-506435) with bound NADP
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 31-ID |
Synchrotron site | APS |
Beamline | 31-ID |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2012-10-18 |
Detector | RAYONIX MX225HE |
Wavelength(s) | 0.9793 |
Spacegroup name | P 43 21 2 |
Unit cell lengths | 93.022, 93.022, 109.285 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 25.800 - 1.350 |
R-factor | 0.1395 |
Rwork | 0.139 |
R-free | 0.15620 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3uf0 |
RMSD bond length | 0.015 |
RMSD bond angle | 1.722 |
Data reduction software | MOSFLM |
Data scaling software | SCALA (3.3.20) |
Phasing software | AMoRE |
Refinement software | PHENIX (1.8.1_1168) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 109.285 | 25.800 | 1.420 |
High resolution limit [Å] | 1.350 | 4.270 | 1.350 |
Rmerge | 0.116 | 0.035 | 0.755 |
Total number of observations | 49525 | 218771 | |
Number of reflections | 105259 | ||
<I/σ(I)> | 15.3 | 16.4 | 1 |
Completeness [%] | 99.9 | 99.4 | 99.8 |
Redundancy | 14.5 | 13.6 | 14.4 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 298 | Protein (10mM Tris, pH 7.9), Reservoir (0.1 M Bis-Tris:HCl, pH 6.5, 2.0 M Ammonium Sulfate, 10 mM NADP), Cryoprotection (Reservoir + 20% Ethylene glycol), vapor diffusion, sitting drop, temperature 298K |