3ZWT

Structure of Human Dihydroorotate Dehydrogenase with a Bound Inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1D3GPDB ENTRY 1D3G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M SODIUM ACETATE (PH 4.8), 2.4-2.6 M AMMONIUM SULPHATE, 40 MM C11DAO, 20 MM DDAO.
Crystal Properties
Matthews coefficientSolvent content
3.6966.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.79α = 90
b = 90.79β = 90
c = 123.491γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.5530.8799.80.08145.38564313.658
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)
11.551.631000.443.75.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1D3G1.5578.6381242427999.690.160290.159390.17744RANDOM13.179
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]
0.30.150.3-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.14
r_dihedral_angle_4_deg17.269
r_dihedral_angle_3_deg12.046
r_dihedral_angle_1_deg5.571
r_scangle_it4.799
r_scbond_it2.84
r_mcangle_it1.887
r_angle_refined_deg1.567
r_mcbond_it1.022
r_angle_other_deg0.941
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.14
r_dihedral_angle_4_deg17.269
r_dihedral_angle_3_deg12.046
r_dihedral_angle_1_deg5.571
r_scangle_it4.799
r_scbond_it2.84
r_mcangle_it1.887
r_angle_refined_deg1.567
r_mcbond_it1.022
r_angle_other_deg0.941
r_mcbond_other0.276
r_chiral_restr0.1
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.002
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_mcangle_other
r_scbond_other
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 Atoms2693
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing