4YS8
Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-G |
Synchrotron site | APS |
Beamline | 21-ID-G |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2015-02-25 |
Detector | MARMOSAIC 300 mm CCD |
Wavelength(s) | 0.97856 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 45.650, 138.310, 78.590 |
Unit cell angles | 90.00, 101.89, 90.00 |
Refinement procedure
Resolution | 29.529 - 2.450 |
R-factor | 0.2181 |
Rwork | 0.216 |
R-free | 0.26290 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1vgw |
RMSD bond length | 0.004 |
RMSD bond angle | 0.780 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | MR-Rosetta |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 2.510 | |
High resolution limit [Å] | 2.450 | 10.960 | 2.450 |
Rmerge | 0.077 | 0.022 | 0.551 |
Rmeas | 0.089 | 0.026 | 0.640 |
Total number of observations | 134066 | ||
Number of reflections | 34999 | 384 | 2593 |
<I/σ(I)> | 14.76 | 38.32 | 2.87 |
Completeness [%] | 99.8 | 92.8 | 100 |
Redundancy | 3.8 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 290 | ButhA.00168.a.A1.PW33338 at 30.46 mg/ml was incuabted with 6mM MgCl2 and 6mM ATP, then mixed 1:1 with JCSG+(e11): 14.4% PEG-8000, 80mM Sodium Cacodylate/ HCl, pH=6.5, 160mM Calcium acetate, 20% glycerol |