6IDJ

Crystal structure of human DHODH in complex with ferulenol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3W7R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.9293100 MM SODIUM ACETATE, 1.8-1.9 M AMMONIUM SULPHATE, 40 MM C11DAO, 20.8 MM DDAO, 2 MM DIHYDROOROTATE,
Crystal Properties
Matthews coefficientSolvent content
3.3963.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.155α = 90
b = 90.155β = 90
c = 123.334γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98000Photon FactoryBL-17A

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
11.9501000.0819.57.546303
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)
11.91.931000.7297.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3W7R1.919.8943740233599.610.163340.162560.17803RANDOM29.991
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]
-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.996
r_dihedral_angle_4_deg16.803
r_dihedral_angle_3_deg13.323
r_long_range_B_other6.201
r_long_range_B_refined6.2
r_dihedral_angle_1_deg5.856
r_scangle_other4.398
r_scbond_it2.663
r_scbond_other2.662
r_mcangle_other2.498
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.996
r_dihedral_angle_4_deg16.803
r_dihedral_angle_3_deg13.323
r_long_range_B_other6.201
r_long_range_B_refined6.2
r_dihedral_angle_1_deg5.856
r_scangle_other4.398
r_scbond_it2.663
r_scbond_other2.662
r_mcangle_other2.498
r_mcangle_it2.497
r_mcbond_it1.628
r_mcbond_other1.608
r_angle_refined_deg1.539
r_angle_other_deg0.969
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2805
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing