9DCP

Structure of PmHMGR bound to mevalonate, CoA and NAD 1 minute 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	225.766, 225.766, 225.766
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	48.130 - 2.060
R-factor	0.2151
Rwork	0.214
R-free	0.24140
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.003
RMSD bond angle	0.537
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	PHASER
Refinement software	PHENIX ((1.21.1_5286))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.150
High resolution limit [Å]	2.060	4.480	2.080
Rmerge	0.162	0.071	4.236
Rmeas	0.165	0.073	4.323
Rpim	0.029	0.013	0.859
Number of reflections	58699	6206	5769
<I/σ(I)>	6.1
Completeness [%]	100.0	100	100
Redundancy	31.1	30.5	25.1
CC(1/2)	0.992	0.998	0.301

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	9	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 for 1 minute at pH 9