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Crystal structure of inactive mutant dUTPase complexed with substrate dUTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUW PDB ENTRY 1EUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 PEG 3350, SODIUM ACETATE, TRIS, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.421 α = 90 b = 76.421 β = 90 c = 100.259 γ = 120
Symmetry Space Group P 63 2 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 MARRESEARCH mirror 2004-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8414 EMBL/DESY, HAMBURG BW7B
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 1.9 20 98.3 0.063 14.97 2.88 13413 13413 -3 32.959
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 1.91 2.03 98.5 0.484 2.54 2.91 2085
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1EUW 1.95 20 12350 12350 645 98.62 0.15971 0.15971 0.15821 0.1886 0.1908 RANDOM 29.501
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] -0.8 -0.4 -0.8 1.21
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 13.55 r_scbond_it 10.344 r_dihedral_angle_1_deg 6.457 r_mcangle_it 3.137 r_angle_refined_deg 1.686 r_mcbond_it 1.466 r_angle_other_deg 0.838 r_symmetry_hbond_refined 0.366 r_symmetry_vdw_other 0.275 r_nbd_other 0.257
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 13.55 r_scbond_it 10.344 r_dihedral_angle_1_deg 6.457 r_mcangle_it 3.137 r_angle_refined_deg 1.686 r_mcbond_it 1.466 r_angle_other_deg 0.838 r_symmetry_hbond_refined 0.366 r_symmetry_vdw_other 0.275 r_nbd_other 0.257 r_xyhbond_nbd_refined 0.24 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.16 r_chiral_restr 0.104 r_nbtor_other 0.087 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1035 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MOLREP phasing