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Structure of B. subtilis genomic dUTPase YncF in complex with dU, PPi and Mg in P1
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 4.6 30% MPD, 0.1 M SODIUM ACETATE PH 4.6, 0.02 M CACL2
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.06 α = 89.72 b = 97.07 β = 88.47 c = 193.85 γ = 90.11
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 2011-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
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 2.01 36.44 96.7 0.09 5.9 2.2 434755 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 2.01 2.06 95.9 0.4 2.4 2.2
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 2.01 36.44 434755 22967 96.74 0.17122 0.16909 0.1741 0.21185 0.2155 RANDOM 22.493
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] -0.36 -0.3 0.01 -0.65 0.32 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.691 r_dihedral_angle_4_deg 16.815 r_dihedral_angle_3_deg 14.992 r_dihedral_angle_1_deg 6.438 r_angle_refined_deg 1.902 r_angle_other_deg 1.31 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.691 r_dihedral_angle_4_deg 16.815 r_dihedral_angle_3_deg 14.992 r_dihedral_angle_1_deg 6.438 r_angle_refined_deg 1.902 r_angle_other_deg 1.31 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.004 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 54570 Nucleic Acid Atoms Solvent Atoms 4726 Heterogen Atoms 1258
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing