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B. subtilis prophage dUTPase YosS in complex with dUMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XCD PDB ENTRY 2XCD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 14% PEG 3350, 0.1 M SODIUM MALONATE, 0.1 M, BIS-TRIS PROPANE PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.2 44.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.82 α = 90 b = 100.01 β = 90 c = 99.51 γ = 90
Symmetry Space Group P 21 21 21
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 CCD 2011-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.6 28.8 99.5 0.08 7.8 5.9 131522 1
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 1.6 1.69 99.9 0.6 2.1 6.4
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 2XCD 1.6 70.65 123669 6577 99.03 0.15347 0.1503 0.1571 0.21365 0.218 RANDOM 21.005
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] -0.09 -0.44 0.53
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.817 r_dihedral_angle_2_deg 33.52 r_dihedral_angle_4_deg 18.007 r_dihedral_angle_3_deg 13.532 r_sphericity_bonded 12.439 r_dihedral_angle_1_deg 6.081 r_rigid_bond_restr 2.716 r_angle_refined_deg 1.446 r_angle_other_deg 0.841 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.817 r_dihedral_angle_2_deg 33.52 r_dihedral_angle_4_deg 18.007 r_dihedral_angle_3_deg 13.532 r_sphericity_bonded 12.439 r_dihedral_angle_1_deg 6.081 r_rigid_bond_restr 2.716 r_angle_refined_deg 1.446 r_angle_other_deg 0.841 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6273 Nucleic Acid Atoms Solvent Atoms 1137 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling