6NMO
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand SR-4
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU FR-E+ SUPERBRIGHT |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2018-12-11 |
Detector | RIGAKU SATURN 944+ |
Wavelength(s) | 1.5418 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 117.080, 67.600, 60.810 |
Unit cell angles | 90.00, 96.48, 90.00 |
Refinement procedure
Resolution | 44.489 - 1.450 |
R-factor | 0.1273 |
Rwork | 0.126 |
R-free | 0.15900 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3qhd native protein |
RMSD bond length | 0.006 |
RMSD bond angle | 0.946 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 44.489 | 44.489 | 1.490 |
High resolution limit [Å] | 1.450 | 6.480 | 1.450 |
Rmerge | 0.028 | 0.015 | 0.352 |
Rmeas | 0.029 | 0.015 | 0.386 |
Total number of observations | 772119 | ||
Number of reflections | 79703 | 986 | 4989 |
<I/σ(I)> | 44.91 | 185.01 | 4.6 |
Completeness [%] | 95.5 | 99.6 | 80.9 |
Redundancy | 9.687 | 20.77 | 5.552 |
CC(1/2) | 1.000 | 1.000 | 0.932 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | Hampton Research Index, condition C9:: 0.5% (V/V) Jeffamine ED-2003, 1100mM sodium malonate dibasic, 100mM HEPES free acid / NaOH pH 7.0: BupsA.00122.a.D11.PD00455 at 22mg/ml + 9mM compound BSI109013/SR-4: cryo: 20% EG and : tray 302690c9: puck: phr5-8 |