4EMD
Crystal structure of IspE (4-diphosphocytidyl-2-C-methyl-D-erythritol kinase) from Mycobacterium abcessus, bound to CMP and SO4
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU FR-E SUPERBRIGHT |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2012-03-29 |
Detector | RIGAKU SATURN 944+ |
Wavelength(s) | 1.541780 |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 46.440, 109.930, 53.100 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 50.000 - 1.750 |
R-factor | 0.161 |
Rwork | 0.159 |
R-free | 0.20400 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4dxl |
RMSD bond length | 0.015 |
RMSD bond angle | 1.530 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | REFMAC |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 1.800 | |
High resolution limit [Å] | 1.750 | 7.830 | 1.750 |
Rmerge | 0.062 | 0.025 | 0.454 |
Number of reflections | 28123 | 374 | 2005 |
<I/σ(I)> | 30.2 | 88 | 2.3 |
Completeness [%] | 99.7 | 99.2 | 97.4 |
Redundancy | 9.25 | 2.54 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 290 | Internal tracking number 230821D4, JCSG screen condition D4: 30% PEG8000, acetate, pH 4.5, 200 mM lithium sulfate, MyabA.00725.a.A1 PW30213 at 29.3 mg/mL in 25 mM HEPES, pH 7.0, 500 mM sodium chloride, 2 mM DTT, 0.025% sodium azide, 5% glycerol, 2 mM CDP, 2 mM ATP, 2 mM meso-erythritol, cryoprotectant: 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 290K |