3FJ6 | pdb_00003fj6

Human dihydroorotate dehydrogenase in complex with a leflunomide derivative inhibitor 2

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	291	drops: 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
3.7	66.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.013	α = 90
b = 91.013	β = 90
c = 123.207	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	1.8	26.82	99.3			55038	54653	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)
	1.8	1.847	93.48

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	PDB ID 1D3H	1.8	26.82	2	49666	48931	5474	98.52	0.17897	0.17897	0.17622	0.18	0.20362	0.2	RANDOM	19.515

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]
0.03	0.01		0.03		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.929
r_dihedral_angle_4_deg	15.573
r_dihedral_angle_3_deg	13.092
r_dihedral_angle_1_deg	5.678
r_scangle_it	3.429
r_scbond_it	2.166
r_angle_refined_deg	1.347
r_mcangle_it	1.314
r_mcbond_it	0.865
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.929
r_dihedral_angle_4_deg	15.573
r_dihedral_angle_3_deg	13.092
r_dihedral_angle_1_deg	5.678
r_scangle_it	3.429
r_scbond_it	2.166
r_angle_refined_deg	1.347
r_mcangle_it	1.314
r_mcbond_it	0.865
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.244
r_symmetry_hbond_refined	0.219
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2790
Nucleic Acid Atoms
Solvent Atoms	419
Heterogen Atoms	78

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.