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Crystal structure of dUTPase H145W mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PY4 PDB entry 2PY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.3 M Ammonium sulfate, 50 mM Tris-HCl, 12 % Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.03 39.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.058 α = 90 b = 55.058 β = 90 c = 83.793 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD Mirrors 2008-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.97861 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.2 20 94.2 0.039 18.4 3.73 42370 -3 16.422
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.23 68.9 0.472 2.02 1.467 2286
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 2PY4 1.2 20 42364 42364 2252 0.1167 0.1167 0.1593 RANDOM
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 s_from_restr_planes 0.407 s_approx_iso_adps 0.078 s_zero_chiral_vol 0.07 s_non_zero_chiral_vol 0.066 s_anti_bump_dis_restr 0.061 s_similar_adp_cmpnt 0.046 s_angle_d 0.029 s_bond_d 0.012 s_rigid_bond_adp_cmpnt 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1162 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 45
Software Software Software Name Purpose MAR345 data collection MOLREP phasing SHELXL-97 refinement XDS data reduction XSCALE data scaling