3FJL | pdb_00003fjl

Human dihydroorotate dehydrogenase in complex with a leflunomide derivative inhibitor 3

X-RAY DIFFRACTION

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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
3.68	66.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.888	α = 90
b = 90.888	β = 90
c = 122.915	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	1.9	78.81	99.56			46965	46758	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.9	78.81	2	46758	42031	4727	99.56	0.18021	0.18021	0.17699	0.18	0.20897	0.21	RANDOM	18.73

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]
0.36	0.18		0.36		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.444
r_dihedral_angle_4_deg	20.381
r_dihedral_angle_3_deg	14.317
r_dihedral_angle_1_deg	5.653
r_scangle_it	3.772
r_scbond_it	2.339
r_mcangle_it	1.424
r_angle_refined_deg	1.413
r_mcbond_it	0.949
r_nbtor_refined	0.3
r_symmetry_vdw_refined	0.265
r_nbd_refined	0.212
r_symmetry_hbond_refined	0.202
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2781
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms	71

Software

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