2FPY

Dual binding mode of a novel series of DHODH inhibitors


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1D3G1D3G.pdb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.7293Drops were formed by mixing equal amounts of 20 mg/ml protein in 50 mM HEPES pH 7.7, 400 mM NaCl, 30% glycerol, 1 mM EDTA and 10 mM N,N-dimethylundecylamin-N-oxide (C11DAO) with a precipitant solution of 0.1 M acetate pH 4.6 5.0, 40 mM C11DAO, 20.8 mM N,N-dimethyldecylamine-N-oxide (DDAO), 2 mM dihydroorotate (DHO), 1.8 2.4 M ammonium sulfate, 1 mM compound. The hanging drops were incubated against 0.5 mL reservoir of 0.1 M acetate pH 4.8, 2.4 2.6 M ammonium sulfate and 30% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3463.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.295α = 90
b = 90.295β = 90
c = 122.695γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.05MPG/DESY, HAMBURGBW6

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
11.91898.60.0652141032118.7
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)
1.92.05990.244.939080

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1D3G.pdb217.2241032196598.50.1810.2RANDOM21.7
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]
1.641.781.64-3.29
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.2
c_scangle_it3.14
c_scbond_it2.08
c_mcangle_it1.64
c_angle_deg1.2
c_mcbond_it1.11
c_improper_angle_d0.8
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2785
Nucleic Acid Atoms
Solvent Atoms291
Heterogen Atoms101

Software

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