3KVL

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with amino-benzoic acid inhibitor 715 at 1.85A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52982.4 M AMMONIUM SULFATE, 15% GLYCEROL, 0.1 M NA-ACETATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.4364.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.695α = 90
b = 90.695β = 90
c = 123.218γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0000APS22-ID

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
11.855099.10.08576.750141
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)
1.851.9299.90.416.34971

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1D3G1.8526.745012348450241895.70.1730.1720.191RANDOM20.259
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]
1.131.121.13-2.26
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.5
c_scangle_it3.22
c_scbond_it2.08
c_mcangle_it1.72
c_mcbond_it1.16
c_angle_deg0.8
c_improper_angle_d0.71
c_bond_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2757
Nucleic Acid Atoms
Solvent Atoms302
Heterogen Atoms89

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
CNXrefinement