4RK8

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with DH03A356


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3JS3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.82930.1M acetate pH 4.8, 40 mM UDAO, 20.8 mM, N,N-dimethyldecylamine-N-oxide (DDAO), 2mM DHO, 1.6-1.8M ammonium sulfate, 1 mM inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.4364.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.82α = 90
b = 90.82β = 90
c = 122.851γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97852SSRFBL17U

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
12.2248.4195.1295452810222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.222.34

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 REPLACEMENTTHROUGHOUT3JS32.2248.412954528102140895.10.143850.142210.17659RANDOM19.225
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]
0.010.010.01-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.008
r_dihedral_angle_4_deg17.519
r_dihedral_angle_3_deg13.877
r_dihedral_angle_1_deg6.319
r_angle_refined_deg2.117
r_angle_other_deg0.904
r_chiral_restr0.102
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_gen_planes_other0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.008
r_dihedral_angle_4_deg17.519
r_dihedral_angle_3_deg13.877
r_dihedral_angle_1_deg6.319
r_angle_refined_deg2.117
r_angle_other_deg0.904
r_chiral_restr0.102
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_gen_planes_other0.007
r_bond_other_d0.002
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
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 Atoms249
Heterogen Atoms125

Software

Software
Software NamePurpose
HKL-2000data collection
automodel building
REFMACrefinement
HKL-2000data reduction
iMOSFLMdata reduction
autophasing