3F4F

Crystal structure of dUT1p, a dUTPase from Saccharomyces cerevisiae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OKDPDB entry 2OKD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52950.2M Na Acetate, 0.1M Tris-HCl pH 8.5, 30% PEG 4000, 10mM d-UTP, 0.015 mg/mL Trypsin. Cryoprotected with 4% Glycerol, 4% Ethylene glycol, 4% Sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9135.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.498α = 90
b = 124.498β = 90
c = 51.664γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Mirrors2008-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54178

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
125099.90.08615.14.3539585395820.5
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)
122.071000.3864.9145381

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 REPLACEMENTTHROUGHOUTPDB entry 2OKD247.7326589140699.930.149410.14640.20713RANDOM24.8
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.497
r_dihedral_angle_4_deg18.013
r_dihedral_angle_3_deg14.044
r_dihedral_angle_1_deg6.476
r_scangle_it3.962
r_scbond_it2.521
r_angle_refined_deg1.655
r_mcangle_it1.279
r_mcbond_it0.73
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.497
r_dihedral_angle_4_deg18.013
r_dihedral_angle_3_deg14.044
r_dihedral_angle_1_deg6.476
r_scangle_it3.962
r_scbond_it2.521
r_angle_refined_deg1.655
r_mcangle_it1.279
r_mcbond_it0.73
r_nbtor_refined0.309
r_nbd_refined0.223
r_symmetry_hbond_refined0.209
r_xyhbond_nbd_refined0.16
r_symmetry_vdw_refined0.131
r_chiral_restr0.128
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms3037
Nucleic Acid Atoms
Solvent Atoms437
Heterogen Atoms83

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling