1ZOR | pdb_00001zor

Isocitrate dehydrogenase from the hyperthermophile Thermotoga maritima

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	291	PEG 6000, Sodium Acetate, Succinate, NaCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.47	α = 90
b = 88.051	β = 90
c = 180.926	γ = 90

Symmetry
Space Group	P 21 21 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	MARRESEARCH		2003-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711	0.996	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	2.24	35.56	99.7	0.066	15.84	4.8	49143	48990	1.38		40.94

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	2.24	2.29	100		0.379	3.32		2500

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1LWD, 1T0L	2.24	35.56	1.38	48988	46511	2477	99.74	0.18647	0.18647	0.18449	0.22317	0.2641	RANDOM	45.332

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]
2.41			-3.05		0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.321
r_dihedral_angle_4_deg	21.497
r_dihedral_angle_3_deg	16.376
r_dihedral_angle_1_deg	6.496
r_scangle_it	2.658
r_scbond_it	1.646
r_angle_refined_deg	1.251
r_mcangle_it	0.87
r_mcbond_it	0.454
r_nbtor_refined	0.303
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.177
r_xyhbond_nbd_refined	0.155
r_metal_ion_refined	0.153
r_symmetry_hbond_refined	0.142
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6358
Nucleic Acid Atoms
Solvent Atoms	428
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing