5K87
crystal structure of malonate bound to methylaconitate isomerase PrpF from Shewanella oneidensis
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 19-ID |
Synchrotron site | APS |
Beamline | 19-ID |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2016-04-08 |
Detector | DECTRIS PILATUS3 X 6M |
Wavelength(s) | 0.979 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 51.825, 103.393, 78.088 |
Unit cell angles | 90.00, 104.47, 90.00 |
Refinement procedure
Resolution | 31.360 - 1.219 |
R-factor | 0.1638 |
Rwork | 0.163 |
R-free | 0.18190 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2pvz |
RMSD bond length | 0.006 |
RMSD bond angle | 1.080 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | REFMAC |
Refinement software | PHENIX (1.9_1692) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 1.240 |
High resolution limit [Å] | 1.220 | 1.220 |
Rmerge | 0.051 | 0.670 |
Number of reflections | 227930 | |
<I/σ(I)> | 49.5 | 2.4 |
Completeness [%] | 96.5 | 84.5 |
Redundancy | 13 | 6.1 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293.15 | 100 mM MES pH 6.0, 136 mM sodium malonate, 15% polyethylene glycol 4000 (PEG 4K) |