2B4G | pdb_00002b4g

dihydroorotate dehydrogenase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JUE	PDB accession code 1JUE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	298	0.4 ul protein 14.1 mg/ml 0.4 ul crystallization buffer, 40% PEG 1000, 0.1M Na Citrate, 0.1M KBr, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2	36.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.605	α = 90
b = 162.63	β = 90
c = 163.07	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC QUANTUM 210		2005-09-05	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9201	ALS	8.2.1

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	1.95	163	96.2	0.107	0.107	6	4.4		76097

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	1.95	2.06			0.428	0.428	1.8

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 (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 accession code 1JUE	1.95	50	75972	72158	3814	96	0.1916	0.18894	0.2	0.24243	0.2	RANDOM	14.022

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]
-0.78			1.08		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.521
r_dihedral_angle_4_deg	15.886
r_dihedral_angle_3_deg	13.928
r_dihedral_angle_1_deg	6.255
r_scangle_it	2.256
r_scbond_it	1.495
r_angle_refined_deg	1.326
r_angle_other_deg	0.837
r_mcangle_it	0.821
r_mcbond_it	0.714
r_symmetry_vdw_refined	0.323
r_symmetry_hbond_refined	0.294
r_symmetry_vdw_other	0.259
r_nbd_refined	0.196
r_nbd_other	0.178
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.168
r_mcbond_other	0.127
r_nbtor_other	0.083
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9572
Nucleic Acid Atoms
Solvent Atoms	638
Heterogen Atoms	203

Software

Software
Software Name	Purpose
SCALA	data scaling
PDB_EXTRACT	data extraction
REFMAC	refinement
CCP4	data scaling
MOLREP	phasing