3G0U | pdb_00003g0u

Human dihydroorotate dehydrogenase in complex with a leflunomide derivative inhibitor 4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D3H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	291	Drops: 20mg/mL protein in 50mM HEPES, pH 7.7, 400mM NaCl, 30% glycerol, 1mM EDTA, 10mM N,N-dimethylundecylamin-N-oxide (C11DAO) precipitant solution: 0.1M acetate pH 4.6-5.0, 40mM C11DAO, 20.8mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM dihydroorotate (DHO), 1.8-2.4M ammonium sulfate, 1mM inhibitors reservoir: 0.1M acetate pH 4.8, 2.4-2.6M ammonium sulfate, 30% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.66	66.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.752	α = 90
b = 90.752	β = 90
c = 122.799	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	MARMOSAIC 225 mm CCD		2006-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.98	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	78.59	99.92			40112	40082	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.052	99.69

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1D3H	2	78.59	2	40082	38077	2005	99.92	0.17128	0.17128	0.1696	0.16	0.20281	0.19	RANDOM	16.538

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]
0.21	0.11		0.21		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.125
r_dihedral_angle_4_deg	20.567
r_dihedral_angle_3_deg	14.202
r_scangle_it	6.573
r_dihedral_angle_1_deg	5.952
r_scbond_it	4.066
r_mcangle_it	2.339
r_angle_refined_deg	2.253
r_mcbond_it	1.435
r_chiral_restr	0.224

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.125
r_dihedral_angle_4_deg	20.567
r_dihedral_angle_3_deg	14.202
r_scangle_it	6.573
r_dihedral_angle_1_deg	5.952
r_scbond_it	4.066
r_mcangle_it	2.339
r_angle_refined_deg	2.253
r_mcbond_it	1.435
r_chiral_restr	0.224
r_bond_refined_d	0.032
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2770
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	66

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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.