1XKD

Ternary complex of Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	291	PEG 6K, Magnesium chloride, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.575	α = 90
b = 107.575	β = 90
c = 171.045	γ = 90

Symmetry
Space Group	P 43 21 2

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	MARRESEARCH		2003-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711	1.089	MAX II	I711

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	2.3	39.7	99.9	0.051	25.42	8.3	45289	45223	1.35	2	45.7

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	2.3	2.34	100		0.367	5.53	7.1	2259

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 1XGV	2.3	39.7	1.35	45149	42860	2289	99.79	0.22722	0.2261	0.24822	RANDOM	26.931

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]
-0.3			-0.3		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.983
r_scangle_it	2.604
r_angle_refined_deg	1.928
r_scbond_it	1.668
r_mcangle_it	0.977
r_mcbond_it	0.54
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.207
r_metal_ion_refined	0.185
r_symmetry_hbond_refined	0.156

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.983
r_scangle_it	2.604
r_angle_refined_deg	1.928
r_scbond_it	1.668
r_mcangle_it	0.977
r_mcbond_it	0.54
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.207
r_metal_ion_refined	0.185
r_symmetry_hbond_refined	0.156
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6568
Nucleic Acid Atoms
Solvent Atoms	196
Heterogen Atoms	124

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
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.