Experiment: 7Q07

Ketol-acid reductoisomerase from Methanothermococcus thermolithotrophicus in the open state with NADP and tartrate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7Q03

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291.15	KARI was crystallized at 13.5 mg/ml in the following buffer 25 mM Tris/HCl pH 7.6, 2 mM dithiothreitol, 10% glycerol. The reservoir was filled with 90 ul crystallization solution (33 % (w/v) PEG 5000 MME, 100 mM MES/NaOH pH 6.5 and 200 mM ammonium sulphate). Drops of 0.7 ul protein with 0.7 ul of crystallisation solution were applied on the shelf. Crystals were firstly soaked in the crystallisation solution supplemented with 20 mM NADP, 50 mM L-Tartrate and 50 mM MgCl2 for 3 minutes, and then soaked in the crystallisation solution supplemented with 30 % v/v glycerol before freezing.

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.827	α = 90
b = 130.827	β = 90
c = 130.827	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2016-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97916	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	46.25	100	0.163	0.168	0.039	0.998	23.7	18.2		19073

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	100		0.528	0.554	0.166	0.385	4.4	10.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7Q03	2.2	41.37	133.59	19073	1005	99.99	0.19	0.1864	0.2061	0.2123	0.2289	30.3423

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2536
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	49

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHENIX	phasing