3ARA

Discovery of Novel Uracil Derivatives as Potent Human dUTPase Inhibitors


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529815%~20% PEG 4000, 0.05M Tris buffer, 0.05M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8757.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.89α = 90
b = 83.263β = 90
c = 89.662γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98IMAGE PLATERIGAKU RAXIS V2006-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32B21SPring-8BL32B2

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
11.710097.50.0485.196805166325
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)
11.71.7699.50.212.64.81

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.761.016461462973335297.460.2150.2150.213650.24038RANDOM23.135
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]
-0.02-0.110.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.104
r_dihedral_angle_4_deg21.461
r_dihedral_angle_3_deg12.774
r_dihedral_angle_1_deg7.189
r_scangle_it5.672
r_scbond_it3.576
r_mcangle_it2.461
r_angle_refined_deg2.256
r_mcbond_it1.521
r_chiral_restr0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.104
r_dihedral_angle_4_deg21.461
r_dihedral_angle_3_deg12.774
r_dihedral_angle_1_deg7.189
r_scangle_it5.672
r_scbond_it3.576
r_mcangle_it2.461
r_angle_refined_deg2.256
r_mcbond_it1.521
r_chiral_restr0.19
r_bond_refined_d0.029
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2922
Nucleic Acid Atoms
Solvent Atoms387
Heterogen Atoms101

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling