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Crystal structure of dUT1p, a dUTPase from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OKD PDB entry 2OKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 0.2M 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 coefficient Solvent content 1.91 35.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.498 α = 90 b = 124.498 β = 90 c = 51.664 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ Mirrors 2008-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 50 99.9 0.086 15.1 4.3 53958 53958 20.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 100 0.386 4.91 4 5381
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2OKD 2 47.73 26589 1406 99.93 0.14941 0.1464 0.1523 0.20713 0.2141 RANDOM 24.8
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.497 r_dihedral_angle_4_deg 18.013 r_dihedral_angle_3_deg 14.044 r_dihedral_angle_1_deg 6.476 r_scangle_it 3.962 r_scbond_it 2.521 r_angle_refined_deg 1.655 r_mcangle_it 1.279 r_mcbond_it 0.73 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.497 r_dihedral_angle_4_deg 18.013 r_dihedral_angle_3_deg 14.044 r_dihedral_angle_1_deg 6.476 r_scangle_it 3.962 r_scbond_it 2.521 r_angle_refined_deg 1.655 r_mcangle_it 1.279 r_mcbond_it 0.73 r_nbtor_refined 0.309 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.209 r_xyhbond_nbd_refined 0.16 r_symmetry_vdw_refined 0.131 r_chiral_restr 0.128 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 Atoms Number Protein Atoms 3037 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 83
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling