5GRI

Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+) and citrate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GRH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	0.2 M sodium citrate, pH 8.0, 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.48	64.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.04	α = 90
b = 112.04	β = 90
c = 144.95	γ = 120

Symmetry
Space Group	P 31 2 1

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 PILATUS3 6M		2015-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	1.0000	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.3	50	98.4	53.7	19.5		46471

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5GRH	2.31	46.01	40334	2138	90.4	0.2424	0.2409	0.2712	RANDOM	44.364

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]
2.09			2.09		-4.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.917
r_dihedral_angle_4_deg	21.152
r_dihedral_angle_3_deg	16.624
r_dihedral_angle_1_deg	5.443
r_angle_refined_deg	0.987
r_angle_other_deg	0.755
r_chiral_restr	0.057
r_bond_refined_d	0.005
r_bond_other_d	0.005
r_gen_planes_refined	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.917
r_dihedral_angle_4_deg	21.152
r_dihedral_angle_3_deg	16.624
r_dihedral_angle_1_deg	5.443
r_angle_refined_deg	0.987
r_angle_other_deg	0.755
r_chiral_restr	0.057
r_bond_refined_d	0.005
r_bond_other_d	0.005
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5039
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data processing
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.