4YLW

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with No.33 compound


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.82930.1M acetate, 40mM UDAO, 20.8mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM DHO, 1.6-1.8M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.4364.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.721α = 90
b = 90.721β = 90
c = 123.02γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDADSC QUANTUM 315r2014-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U1.0SSRFBL17U

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
11.7928.6499.8911.710.153848
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)
11.791.8299.890.5135.710.1

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 REPLACEMENTTHROUGHOUT4JTS1.7928.6453848199599.890.155450.154610.17822RANDOM22.646
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.586
r_dihedral_angle_4_deg20.642
r_dihedral_angle_3_deg12.866
r_long_range_B_other8.646
r_long_range_B_refined8.644
r_scangle_other6.786
r_dihedral_angle_1_deg6.491
r_scbond_it4.915
r_scbond_other4.913
r_mcangle_it3.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.586
r_dihedral_angle_4_deg20.642
r_dihedral_angle_3_deg12.866
r_long_range_B_other8.646
r_long_range_B_refined8.644
r_scangle_other6.786
r_dihedral_angle_1_deg6.491
r_scbond_it4.915
r_scbond_other4.913
r_mcangle_it3.332
r_mcangle_other3.331
r_angle_refined_deg2.466
r_mcbond_it2.362
r_mcbond_other2.36
r_angle_other_deg0.991
r_chiral_restr0.141
r_bond_refined_d0.026
r_gen_planes_refined0.014
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms2785
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPmodel building
MOLREPphasing