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Structure of the Bacillus subtilis prophage dUTPase, YosS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DUT PDB ENTRY 1DUT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.1M IMIDAZOLEMALATE BUFFER PH 5.5, 30% (V/V) PEG600
Crystal Properties Matthews coefficient Solvent content 2.19 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.763 α = 90 b = 102.763 β = 90 c = 86.174 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 ADSC QUANTUM 315r 2000-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.74 88.99 99.5 0.06 24.5 5.7 52906 2
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 1.76 1.8 94 0.45 2.3 2.8
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 1DUT 1.74 10 49805 2678 99.78 0.17372 0.17137 0.1933 0.21857 0.2059 RANDOM 23.266
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] -0.79 -0.39 -0.79 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.819 r_dihedral_angle_3_deg 15.515 r_dihedral_angle_4_deg 14.515 r_dihedral_angle_1_deg 6.598 r_scangle_it 5.095 r_scbond_it 3.322 r_mcangle_it 2.034 r_angle_refined_deg 1.91 r_mcbond_it 1.198 r_angle_other_deg 0.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.819 r_dihedral_angle_3_deg 15.515 r_dihedral_angle_4_deg 14.515 r_dihedral_angle_1_deg 6.598 r_scangle_it 5.095 r_scbond_it 3.322 r_mcangle_it 2.034 r_angle_refined_deg 1.91 r_mcbond_it 1.198 r_angle_other_deg 0.993 r_mcbond_other 0.42 r_chiral_restr 0.125 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4077 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing