3INM

Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H mutant in complex with NADPH, ALPHA-KETOGLUTARATE and CALCIUM(2+)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T0L	PDB ENTRY 1T0L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	Protein component: 8 mg/ml IDH, 20mM Tris-HCl pH 7.5, 100mM sodium chloride, 10mM NADPH, 10mM calcium chloride, 75mM alpha-ketoglutaric acid sodium salt. Precipitant: 100mM MES pH 6.5, 20% PEG 6000. Ratio of protein component to precipitant in initial hanging drop: 2:1., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.12	α = 90
b = 274.69	β = 90
c = 116.5	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r	MIRROR AND MONOCHROMETER	2009-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0809	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	25	92.4	0.08	20.3	8.6	89958	83121			31

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	58.8		0.305	2.4	2.1	5232

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 1T0L	2.1	24.91	83109	78956	4153	92.36	0.222	0.22	0.262	RANDOM	33.273

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]
0.03					-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.825
r_dihedral_angle_4_deg	25.226
r_dihedral_angle_3_deg	19.723
r_dihedral_angle_1_deg	6.858
r_scangle_it	3.774
r_scbond_it	2.321
r_mcangle_it	1.318
r_angle_refined_deg	1.105
r_mcbond_it	0.698
r_chiral_restr	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.825
r_dihedral_angle_4_deg	25.226
r_dihedral_angle_3_deg	19.723
r_dihedral_angle_1_deg	6.858
r_scangle_it	3.774
r_scbond_it	2.321
r_mcangle_it	1.318
r_angle_refined_deg	1.105
r_mcbond_it	0.698
r_chiral_restr	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9706
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	198

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

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.