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B. subtilis dUTPase YncF in complex with dU, PPi and Mg (P212121)
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 5 0.2M NACL, 0.1M NA ACETATE PH 5, 20% PEG 6K
Crystal Properties Matthews coefficient Solvent content 2.35 47.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.27 α = 90 b = 71.534 β = 90 c = 92.299 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 2012-03-08 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 2.05 50.13 99.4 0.1 16.7 7.3 29682 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 2.05 2.16 96.9 0.3 4.4 4.4
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 2.05 56.54 28124 1501 99.24 0.16169 0.15898 0.1646 0.21288 0.2187 RANDOM 12.119
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] -0.98 0.49 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.719 r_dihedral_angle_4_deg 17.836 r_dihedral_angle_3_deg 14.16 r_dihedral_angle_1_deg 6.562 r_scangle_it 3.675 r_scbond_it 2.282 r_angle_refined_deg 1.612 r_mcangle_it 1.347 r_angle_other_deg 0.861 r_mcbond_it 0.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.719 r_dihedral_angle_4_deg 17.836 r_dihedral_angle_3_deg 14.16 r_dihedral_angle_1_deg 6.562 r_scangle_it 3.675 r_scbond_it 2.282 r_angle_refined_deg 1.612 r_mcangle_it 1.347 r_angle_other_deg 0.861 r_mcbond_it 0.741 r_mcbond_other 0.177 r_chiral_restr 0.09 r_bond_refined_d 0.015 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_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 3304 Nucleic Acid Atoms Solvent Atoms 566 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing