3ECY

Crystal structural analysis of Drosophila melanogaster dUTPase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.629750 mM sodium succinate buffer, 200 mM sodium chloride, 30-35% methyl-pentane diol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthew coefficientSolvent content
2.2344.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.799α = 90
b = 42.799β = 90
c = 169.384γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.8457EMBL/DESY, HamburgBW7B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.782099.10.06814.957.452822928229-341.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.8995.60.742.36.844348

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 1Q5U1.88202334523345122599.770.201520.200480.22221RANDOM41.067
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]
0.620.62-1.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.792
r_dihedral_angle_3_deg15.143
r_dihedral_angle_4_deg15.038
r_dihedral_angle_1_deg7.84
r_scangle_it7.069
r_scbond_it4.471
r_mcangle_it3.096
r_mcbond_it2.17
r_angle_refined_deg1.938
r_nbtor_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.792
r_dihedral_angle_3_deg15.143
r_dihedral_angle_4_deg15.038
r_dihedral_angle_1_deg7.84
r_scangle_it7.069
r_scbond_it4.471
r_mcangle_it3.096
r_mcbond_it2.17
r_angle_refined_deg1.938
r_nbtor_refined0.318
r_symmetry_vdw_refined0.283
r_nbd_refined0.244
r_symmetry_hbond_refined0.238
r_xyhbond_nbd_refined0.204
r_chiral_restr0.138
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_symmetry_vdw_other
r_nbd_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_angle_other_deg
r_mcbond_other
r_nbtor_other
r_gen_planes_other
r_bond_other_d
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1770
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing