4ZL1

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with 18X at 1.86 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

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, 1mM inhibitor
Crystal Properties
Matthews coefficientSolvent content
3.4764.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.319α = 90
b = 91.319β = 90
c = 122.824γ = 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 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
11.8629.0499.861.310.747711
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.90898.99

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 REPLACEMENTTHROUGHOUT4JTU1.8629.0447711255399.860.16090.159930.17893RANDOM23.267
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_deg35.536
r_dihedral_angle_4_deg18.257
r_dihedral_angle_3_deg13.607
r_long_range_B_refined7.34
r_long_range_B_other7.339
r_dihedral_angle_1_deg6.198
r_scangle_other5.873
r_scbond_it4.172
r_scbond_other4.016
r_mcangle_it3.434
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.536
r_dihedral_angle_4_deg18.257
r_dihedral_angle_3_deg13.607
r_long_range_B_refined7.34
r_long_range_B_other7.339
r_dihedral_angle_1_deg6.198
r_scangle_other5.873
r_scbond_it4.172
r_scbond_other4.016
r_mcangle_it3.434
r_mcangle_other3.434
r_mcbond_it2.535
r_mcbond_other2.529
r_angle_refined_deg2.264
r_angle_other_deg0.978
r_chiral_restr0.141
r_bond_refined_d0.026
r_gen_planes_refined0.013
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 Atoms2792
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
Cootmodel building