5YVZ
Crystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate dependent dioxygenase in complex with alphaketoglutarate and Fe(III)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 22-BM |
Synchrotron site | APS |
Beamline | 22-BM |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2012-04-16 |
Detector | MARMOSAIC 225 mm CCD |
Wavelength(s) | 1.0 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 45.710, 59.204, 116.264 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 34.547 - 1.600 |
R-factor | 0.1607 |
Rwork | 0.160 |
R-free | 0.18220 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5Y7S |
RMSD bond length | 0.005 |
RMSD bond angle | 0.790 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | PHENIX |
Refinement software | PHENIX (1.10.1_2155) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.630 |
High resolution limit [Å] | 1.600 | 4.340 | 1.600 |
Rmerge | 0.104 | 0.083 | 0.468 |
Number of reflections | 41701 | 2309 | 1828 |
<I/σ(I)> | 11.9 | ||
Completeness [%] | 98.2 | 99.1 | 86.5 |
Redundancy | 10 | 10 | 7.3 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 288 | 0.1M Sodium acetate (pH=4.5), 200mM Lithium sulfate, 50 % v/v PEG 400 |