Experiment: 1V94

Crystal structure of isocitrate dehydrogenase from Aeropyrum pernix

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ICD	PDB ENTRY 4ICD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	298	PEG3350, ammonium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.62	52.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.863	α = 90
b = 107.863	β = 90
c = 172.858	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	ADSC QUANTUM 4		2003-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	1.000	Photon Factory	BL-6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.28	50	99.7	0.07	31.3	7.9	47317	47175			30.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.28	2.36	99.4		0.244	5.3	7.5	4600

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 (All)	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	PDB ENTRY 4ICD	2.28	45.98	47175	47110	2354		0.217	0.215	0.215	0.2172	0.256	0.2092	RANDOM	42.4

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]
1.38			1.38		-2.76

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.8
c_scangle_it	4.29
c_scbond_it	3.11
c_mcangle_it	2.83
c_mcbond_it	1.95
c_angle_deg	1.2
c_improper_angle_d	0.87
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6617
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing