3G0U

Human dihydroorotate dehydrogenase in complex with a leflunomide derivative inhibitor 4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1D3H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.8291Drops: 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 coefficientSolvent content
3.6666.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.752α = 90
b = 90.752β = 90
c = 122.799γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.98ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1278.5999.92401124008222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.05299.69

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1D3H278.5924008238077200599.920.171280.171280.16960.20281RANDOM16.538
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]
0.210.110.21-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.125
r_dihedral_angle_4_deg20.567
r_dihedral_angle_3_deg14.202
r_scangle_it6.573
r_dihedral_angle_1_deg5.952
r_scbond_it4.066
r_mcangle_it2.339
r_angle_refined_deg2.253
r_mcbond_it1.435
r_chiral_restr0.224
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.125
r_dihedral_angle_4_deg20.567
r_dihedral_angle_3_deg14.202
r_scangle_it6.573
r_dihedral_angle_1_deg5.952
r_scbond_it4.066
r_mcangle_it2.339
r_angle_refined_deg2.253
r_mcbond_it1.435
r_chiral_restr0.224
r_bond_refined_d0.032
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2770
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms66

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling