2QFW

Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate dehydrogenase in complex with isocitrate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	293	0.1M HEPES-Na, 0.2M Li2SO4, 0.1M NaF, 20% PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.699	α = 90
b = 97.886	β = 98.95
c = 190.651	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	IMAGE PLATE	RIGAKU RAXIS IV++	MSC confocal max-flux optics	2005-08-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.6	19.9	98.4	0.06	0.06	9	2.62		82166			64.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.69	99.9		0.228	0.06	2	2.66	8296

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	1LWD	2.6	20	82147	4154	98.38	0.235	0.232	0.292	RANDOM	51.646

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]
1.39		-2.13	-0.79		-1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	3.941
r_scangle_it	2.166
r_mcangle_it	1.319
r_scbond_it	1.192
r_angle_refined_deg	0.89
r_mcbond_it	0.693
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.159
r_xyhbond_nbd_refined	0.107
r_symmetry_hbond_refined	0.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	3.941
r_scangle_it	2.166
r_mcangle_it	1.319
r_scbond_it	1.192
r_angle_refined_deg	0.89
r_mcbond_it	0.693
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.159
r_xyhbond_nbd_refined	0.107
r_symmetry_hbond_refined	0.099
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19452
Nucleic Acid Atoms
Solvent Atoms	1158
Heterogen Atoms	78

Software

Software
Software Name	Purpose
d*TREK	data scaling
CNS	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CNS	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 R01GM133198.