3F1Q

Human dihydroorotate dehydrogenase in complex with a leflunomide derivative inhibitor 1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.8293drops: 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 293K
Crystal Properties
Matthews coefficientSolvent content
3.6666.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.696α = 90
b = 90.696β = 90
c = 122.95γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.98ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
1230.741000.08814.35.640134401342214.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.111000.2386.15.65807

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1D3H229.693808336072201199.960.179470.178390.19937RANDOM5.209
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]
0.290.150.29-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.623
r_dihedral_angle_4_deg18.647
r_dihedral_angle_3_deg13.143
r_dihedral_angle_1_deg5.229
r_scangle_it1.823
r_angle_refined_deg1.085
r_scbond_it1.081
r_mcangle_it0.394
r_nbtor_refined0.298
r_symmetry_hbond_refined0.278
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.623
r_dihedral_angle_4_deg18.647
r_dihedral_angle_3_deg13.143
r_dihedral_angle_1_deg5.229
r_scangle_it1.823
r_angle_refined_deg1.085
r_scbond_it1.081
r_mcangle_it0.394
r_nbtor_refined0.298
r_symmetry_hbond_refined0.278
r_mcbond_it0.257
r_nbd_refined0.196
r_symmetry_vdw_refined0.19
r_xyhbond_nbd_refined0.129
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2758
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms76

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling