4XUD

Synthesis and evaluation of heterocyclic catechol mimics as inhibitors of catechol-O-methyltransferase (COMT): Structure with Cmpd32 ([1-(biphenyl-3-yl)-5-hydroxy-4-oxo-1,4-dihydropyridin-3-yl]boronic acid)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72980.1M HEPES, 30% PEG 6000; MA000474 (JCSG core IV), drop e12 :100uM ligand, 12mg/ml protein
Crystal Properties
Matthews coefficientSolvent content
2.5651.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.812α = 90
b = 57.631β = 90
c = 98.249γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2008-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54

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
12.4501000.1987.27.710266
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)
12.42.441000.6967.7505

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 REPLACEMENTTHROUGHOUT4XUC2.449.69961148498.660.17130.16790.241RANDOM24.293
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]
1.66-0.75-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.931
r_dihedral_angle_3_deg13.893
r_dihedral_angle_4_deg10.626
r_dihedral_angle_1_deg5.734
r_scangle_it2.743
r_scbond_it1.681
r_angle_refined_deg1.316
r_mcangle_it1.025
r_mcbond_it0.618
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.931
r_dihedral_angle_3_deg13.893
r_dihedral_angle_4_deg10.626
r_dihedral_angle_1_deg5.734
r_scangle_it2.743
r_scbond_it1.681
r_angle_refined_deg1.316
r_mcangle_it1.025
r_mcbond_it0.618
r_nbtor_refined0.305
r_symmetry_vdw_refined0.202
r_nbd_refined0.188
r_symmetry_hbond_refined0.184
r_xyhbond_nbd_refined0.164
r_chiral_restr0.084
r_metal_ion_refined0.017
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1699
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms63

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing