6OC0

Crystal structure of human DHODH with OSU-03012


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OQV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5293Ammonium sulfate, glycerol, DHO, DDAO, OSU-03012
Crystal Properties
Matthews coefficientSolvent content
3.7266.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.006α = 90
b = 91.006β = 90
c = 123.069γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2018-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.999873APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
11.450990.070.99919.219.53114363
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4894.20.5450.8782.766.52

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 REPLACEMENTTHROUGHOUT4OQV1.448.55107176562297.660.15240.150780.18409RANDOM22.869
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]
-0.69-0.35-0.692.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.741
r_dihedral_angle_4_deg20.111
r_dihedral_angle_3_deg12.702
r_rigid_bond_restr11.419
r_long_range_B_refined8.137
r_long_range_B_other8.102
r_scangle_other7.984
r_mcangle_it6.808
r_mcangle_other6.806
r_scbond_it6.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.741
r_dihedral_angle_4_deg20.111
r_dihedral_angle_3_deg12.702
r_rigid_bond_restr11.419
r_long_range_B_refined8.137
r_long_range_B_other8.102
r_scangle_other7.984
r_mcangle_it6.808
r_mcangle_other6.806
r_scbond_it6.8
r_scbond_other6.798
r_dihedral_angle_1_deg6.617
r_mcbond_it5.75
r_mcbond_other5.749
r_angle_refined_deg1.711
r_angle_other_deg1.7
r_chiral_restr0.083
r_bond_other_d0.018
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.008
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2785
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms91

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building
MOLREPphasing
XDSdata scaling