5HIN

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with 18L compound


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.82930.1M acetate, 40mM C11DAO, 20.8mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM DHO, 1.6-1.8 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.4264.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.734α = 90
b = 90.734β = 90
c = 122.629γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252015-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.987SSRFBL19U1

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
11.628.5699.6519.810.875091

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.628.5675091200199.650.163860.163370.18217RANDOM22.369
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
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.836
r_dihedral_angle_4_deg19.262
r_dihedral_angle_3_deg13.166
r_long_range_B_refined7.469
r_long_range_B_other7.469
r_scangle_other6.21
r_dihedral_angle_1_deg6.109
r_scbond_it4.224
r_scbond_other4.224
r_mcangle_other3.258
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.836
r_dihedral_angle_4_deg19.262
r_dihedral_angle_3_deg13.166
r_long_range_B_refined7.469
r_long_range_B_other7.469
r_scangle_other6.21
r_dihedral_angle_1_deg6.109
r_scbond_it4.224
r_scbond_other4.224
r_mcangle_other3.258
r_mcangle_it3.257
r_angle_refined_deg2.898
r_mcbond_it2.509
r_mcbond_other2.452
r_angle_other_deg1.121
r_chiral_restr0.163
r_bond_refined_d0.031
r_gen_planes_refined0.017
r_gen_planes_other0.005
r_bond_other_d0.001
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 Atoms2792
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms107

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXdata reduction
HKL-3000data scaling
Cootphasing