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