5GRE | pdb_00005gre

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

X-RAY DIFFRACTION

Starting Model(s)

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

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
3.08	60

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.91	α = 90
b = 104.91	β = 90
c = 146.25	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	2.65	50	99.9	22.4	9.1		27500

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	2.65	2.74

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5GRI	2.65	45.43	26073	1382	99.73	0.1971	0.1947	0.2	0.2414	0.25	RANDOM	49.333

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]
3.69			3.69		-7.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.226
r_dihedral_angle_4_deg	18.568
r_dihedral_angle_3_deg	17.339
r_mcangle_it	6.877
r_dihedral_angle_1_deg	5.694
r_mcbond_it	4.709
r_mcbond_other	4.679
r_angle_refined_deg	1.347
r_angle_other_deg	1.01
r_chiral_restr	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.226
r_dihedral_angle_4_deg	18.568
r_dihedral_angle_3_deg	17.339
r_mcangle_it	6.877
r_dihedral_angle_1_deg	5.694
r_mcbond_it	4.709
r_mcbond_other	4.679
r_angle_refined_deg	1.347
r_angle_other_deg	1.01
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_bond_other_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5042
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
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.