5GRH

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M HEPES-Na, pH7.5, 50 mM MgCl2, 30%(v/v) PEGMME 550

Crystal Properties
Matthews coefficient	Solvent content
3.83	67.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.397	α = 90
b = 118.397	β = 90
c = 143.163	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	2.8	19.71	98.9	9.6	10.8		28718

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	2.8	2.9

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	1T09	2.8	19.71	27226	1463	98.57	0.2257	0.2239	0.2592	RANDOM	58.397

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]
14.1			14.1		-28.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.303
r_dihedral_angle_4_deg	20.197
r_dihedral_angle_3_deg	16.021
r_dihedral_angle_1_deg	5.049
r_angle_refined_deg	1.088
r_angle_other_deg	0.731
r_chiral_restr	0.058
r_bond_refined_d	0.006
r_bond_other_d	0.005
r_gen_planes_refined	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.303
r_dihedral_angle_4_deg	20.197
r_dihedral_angle_3_deg	16.021
r_dihedral_angle_1_deg	5.049
r_angle_refined_deg	1.088
r_angle_other_deg	0.731
r_chiral_restr	0.058
r_bond_refined_d	0.006
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	5064
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	1

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.