6V3M
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in compomplex with ligand HGN-0961 (BSI110840)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU FR-E+ SUPERBRIGHT |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2019-11-07 |
Detector | RIGAKU SATURN 944+ |
Wavelength(s) | 1.5418 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 117.310, 67.550, 60.570 |
Unit cell angles | 90.00, 96.32, 90.00 |
Refinement procedure
Resolution | 44.390 - 1.550 |
R-factor | 0.1454 |
Rwork | 0.145 |
R-free | 0.16930 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3qhd |
RMSD bond length | 0.010 |
RMSD bond angle | 1.169 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHENIX |
Refinement software | PHENIX (1.17.1) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.590 |
High resolution limit [Å] | 1.550 | 6.930 | 1.550 |
Rmerge | 0.026 | 0.016 | 0.320 |
Rmeas | 0.027 | 0.016 | 0.360 |
Number of reflections | 67221 | 806 | 4704 |
<I/σ(I)> | 49.7 | 167 | 4.47 |
Completeness [%] | 98.5 | 99.6 | 93.2 |
Redundancy | 11.388 | 20.552 | 4.565 |
CC(1/2) | 1.000 | 0.999 | 0.941 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 290 | Bups122_opt3 screen: 100mM HEPES free acid / NaOH pH 7.4, 200mM ammonium acetate, 27% (w/V) PEG 3350: BupsA.00122.a.A1.PW28612 at 14.33mg/ml plus 1mM ZnCl2 and 10mM compound HGN-0961/BSI110840: soaked over night with reservoir and 25mM compound: cryo: 20% EG + soak buffer: tray 310506a10: puck bno0-4. The ligand description was generated from a smiles string using phenix elbow. The ligand structure was minimized using GAMESS with the 3-21G basis. Restraints were extracted using phenix.elbow |