9DPG

Structure of PmHMGR bound to mevalonate, CoA and NAD 2 minutes 20 seconds after reaction initiation at pH 9

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 23-ID-D
Synchrotron site	APS
Beamline	23-ID-D
Temperature [K]	100
Detector technology	PIXEL
Collection date	2018-08-03
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	1.0332
Spacegroup name	I 41 3 2
Unit cell lengths	224.162, 224.162, 224.162
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	47.790 - 2.500
R-factor	0.1919
Rwork	0.190
R-free	0.23860
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.002
RMSD bond angle	0.455
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	PHASER (v4.2)
Refinement software	PHENIX (1.21.1_5286)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.590
High resolution limit [Å]	2.500	5.380	2.500
Rmerge	0.131	0.049	0.952
Rmeas	0.082	0.052	1.017
Rpim	0.027	0.017	0.351
Number of reflections	33303	3546	3270
<I/σ(I)>	10.01
Completeness [%]	99.9	99.7	100
Redundancy	9	8.6	8.1
CC(1/2)	0.994	0.998	0.713

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.7	293.15	1.2 M ammonium sulfate, 100 mM N-(2-acetamido)iminodiacetic acid, and 10% glycerol. Crystals were buffer exchanged into 1.2 M ammonium acetate, 100 mM ADA, and 10% PEG-400 buffer at pH 6.7 (pH-jump buffer), followed by soaking with 1 mM NAD, mevalonate, and CoA in the pH-jump buffer at pH 9 for 2 min 20 seconds