4OQV | pdb_00004oqv

High resolution crystal structure of human dihydroorotate dehydrogenase bound with DSM338 (N-[3,5-difluoro-4-(trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	293	1.76 M Ammonium sulfate, 0.1 M Sodium Acetate, pH 5.4, 1.9 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.54	65.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.936	α = 90
b = 90.936	β = 90
c = 121.938	γ = 120

Symmetry
Space Group	P 32 2 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 QUANTUM 315		2011-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.979	APS	19-ID

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	1.23	50	99.8	0.057	29.6	7.1	168450	168235	2.7	2.7	10.6

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)
1	1.23	1.25	100		0.612	2.7	6	8270

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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		THROUGHOUT	1.23	30	159728	8445	99.7	0.14217	0.14137	0.14	0.15741	0.16	RANDOM	21.67

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]
-0.13	-0.07		-0.13		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	82.092
r_dihedral_angle_2_deg	34.899
r_sphericity_bonded	23.709
r_dihedral_angle_4_deg	15.076
r_dihedral_angle_3_deg	13.054
r_rigid_bond_restr	9.041
r_dihedral_angle_1_deg	6.154
r_angle_refined_deg	2.488
r_angle_other_deg	1.303
r_chiral_restr	0.156

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	82.092
r_dihedral_angle_2_deg	34.899
r_sphericity_bonded	23.709
r_dihedral_angle_4_deg	15.076
r_dihedral_angle_3_deg	13.054
r_rigid_bond_restr	9.041
r_dihedral_angle_1_deg	6.154
r_angle_refined_deg	2.488
r_angle_other_deg	1.303
r_chiral_restr	0.156
r_bond_refined_d	0.029
r_gen_planes_refined	0.021
r_gen_planes_other	0.015
r_bond_other_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2703
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	90

Software

Software
Software Name	Purpose
HKL-3000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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 R01GM157729.