6MWK
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0883
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU FR-E+ SUPERBRIGHT |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2018-06-07 |
Detector | RIGAKU SATURN 944+ |
Wavelength(s) | 1.5418 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 117.330, 68.040, 60.670 |
Unit cell angles | 90.00, 96.46, 90.00 |
Refinement procedure
Resolution | 40.935 - 1.800 |
R-factor | 0.1434 |
Rwork | 0.142 |
R-free | 0.17850 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3qhd |
RMSD bond length | 0.007 |
RMSD bond angle | 0.942 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX ((dev_3297)) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 40.935 | 40.935 | 1.850 |
High resolution limit [Å] | 1.800 | 8.050 | 1.800 |
Rmerge | 0.102 | 0.036 | 0.509 |
Rmeas | 0.118 | 0.042 | 0.633 |
Number of reflections | 43844 | 506 | 3179 |
<I/σ(I)> | 17.88 | 81.51 | 2.09 |
Completeness [%] | 99.4 | 94.6 | 97.7 |
Redundancy | 3.076 | 3.723 | 1.973 |
CC(1/2) | 0.997 | 0.999 | 0.830 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | Hampton research Index screen, condition C9: 5% Jeffamine ED-2003, 1100mM sodium malonate dibasic, 100mM HEPES free acid / NaOH pH 7.5: BupsA.00122.a.A1.PW28612 at 14mg/ml + 9mM compound bsi108673/HGN-0883: Cryo: 20% EG: Tray 300532c9, puck ZRJ4-4 |