2UXQ

Isocitrate dehydrogenase from the psychrophilic bacterium Desulfotalea psychrophila: biochemical properties and crystal structure analysis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.4		100 MM TRIS/HCL BUFFER PH 7.4, 1.7-1.9 M AMMONIUM SULPHATE, 2% PEG 400, 60 MM MGSO4

Crystal Properties
Matthews coefficient	Solvent content
2.6	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.324	α = 98.9
b = 73.279	β = 98.98
c = 126.413	γ = 113.88

Symmetry
Space Group	P 1

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 CCD	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.75	55	86.3	0.05	9.9	2.1		162467			19.2

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	1.75	1.84	45.7		0.28	2.6	2.1

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	PDB ENTRY 1LWD	1.75	20	159104	3240	86.3	0.146	0.146	0.189	RANDOM	15.57

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]
-0.09	-0.07	-0.01	-0.02	0.05	0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.22
r_dihedral_angle_4_deg	18.658
r_dihedral_angle_3_deg	12.806
r_dihedral_angle_1_deg	6.441
r_scangle_it	3.292
r_scbond_it	2.474
r_angle_refined_deg	1.638
r_mcangle_it	1.408
r_mcbond_it	1.22
r_angle_other_deg	0.893
r_symmetry_vdw_other	0.262
r_nbd_refined	0.214
r_symmetry_hbond_refined	0.199
r_xyhbond_nbd_refined	0.187
r_nbd_other	0.185
r_nbtor_refined	0.176
r_symmetry_vdw_refined	0.132
r_chiral_restr	0.102
r_nbtor_other	0.086
r_bond_refined_d	0.019
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12799
Nucleic Acid Atoms
Solvent Atoms	1883
Heterogen Atoms	146

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing