4ZDQ
Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis complexed with CTP
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 | 2015-04-08 |
Detector | MARMOSAIC 300 mm CCD |
Wavelength(s) | 0.97857 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 45.900, 138.950, 76.920 |
Unit cell angles | 90.00, 101.94, 90.00 |
Refinement procedure
Resolution | 26.932 - 2.300 |
R-factor | 0.2074 |
Rwork | 0.205 |
R-free | 0.25710 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 4ys8 |
RMSD bond length | 0.002 |
RMSD bond angle | 0.563 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHENIX |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 2.360 | |
High resolution limit [Å] | 2.300 | 10.290 | 2.300 |
Rmerge | 0.081 | 0.031 | 0.539 |
Rmeas | 0.094 | 0.037 | 0.626 |
Total number of observations | 159992 | ||
Number of reflections | 41718 | 465 | 3058 |
<I/σ(I)> | 13.44 | 35.65 | 2.84 |
Completeness [%] | 99.7 | 94.5 | 99.6 |
Redundancy | 3.8 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.05 | 290 | ButhA.00168.a.A1.PW33338 at 30.46 mg/ml mixed 1:1 with JCSG+(e11): 10.73% PEG-8000, 80mM Sodium Cacodylate/ HCl, pH=6.04, 160mM Calcium acetate, 20% glycerol. Apo crystals were soaked with 1mM MgCl2, CTP, and D-erythritol-4-phosphate |