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B. subtilis dUTPase YncF in complex with dU PPi and Mg in H32
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 6.5 30% MPD, 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M MAGNESIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.08 40.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.628 α = 90 b = 146.628 β = 90 c = 144.8 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 225 mm CCD 2011-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.3 70 100 0.13 22.64 11.3 26728 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 2.3 2.34 100 0.75 3.2 11
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 2.3 95.47 25311 1343 99.7 0.16553 0.16265 0.1663 0.21861 0.2237 RANDOM 26.698
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] -0.03 -0.02 -0.03 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.874 r_dihedral_angle_3_deg 17.266 r_dihedral_angle_4_deg 16.833 r_dihedral_angle_1_deg 6.702 r_angle_refined_deg 1.863 r_angle_other_deg 0.915 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.874 r_dihedral_angle_3_deg 17.266 r_dihedral_angle_4_deg 16.833 r_dihedral_angle_1_deg 6.702 r_angle_refined_deg 1.863 r_angle_other_deg 0.915 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.006 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4551 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing