5VCP
Crystal structure of a peptide deformylase from Burkholderia xenovorans in complex with actinonin
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-F |
Synchrotron site | APS |
Beamline | 21-ID-F |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2016-02-24 |
Detector | MARMOSAIC 225 mm CCD |
Wavelength(s) | 0.97872 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 63.110, 90.330, 140.210 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 48.536 - 1.950 |
R-factor | 0.1625 |
Rwork | 0.162 |
R-free | 0.19180 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5kob |
RMSD bond length | 0.007 |
RMSD bond angle | 1.062 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.8.4_1496) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 48.536 | 48.536 | 2.000 |
High resolution limit [Å] | 1.950 | 8.720 | 1.950 |
Rmerge | 0.040 | 0.021 | 0.530 |
Rmeas | 0.044 | 0.023 | 0.578 |
Total number of observations | 362861 | ||
Number of reflections | 59117 | 711 | 4328 |
<I/σ(I)> | 23.88 | 56.67 | 3.79 |
Completeness [%] | 99.8 | 93.4 | 100 |
Redundancy | 6.138 | 5.093 | 6.205 |
CC(1/2) | 1.000 | 0.999 | 0.944 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | 1:1 22 mg/mL BuxeA.00078.a.B1.PS37823 / Rigaku reagents Morpheus A8 (0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M HEPES/MOPS, pH 7.5, 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), crystal id: wda5-2 270123a8 |