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Phage dUTPases control transfer of virulence genes by a proto-oncogenic G protein-like mechanism. (Staphylococcus bacteriophage 80alpha dUTPase D81A D110C S168C mutant with dUpNHpp).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZEZ PDB ENTRY 3ZEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2-8% TERT-BUTANOL, 0.1M TRID (PH 8.5). 30-50% MPD OR PEG400.
Crystal Properties Matthews coefficient Solvent content 2.43 49.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.46 α = 90 b = 87.46 β = 90 c = 87.46 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF 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 2.6 39.11 99.9 0.05 23.2 5.5 7102 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 2.6 2.74 100 0.4 3.9 5.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3ZEZ 2.6 35.71 6578 500 99.79 0.22758 0.22429 0.27328 0.2615 RANDOM 63.086
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] -9.01 0.78 -6.2 -9.99 -6.42 19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.793 r_dihedral_angle_3_deg 13.969 r_dihedral_angle_4_deg 12.667 r_dihedral_angle_1_deg 4.632 r_mcangle_it 2.192 r_mcbond_it 1.175 r_angle_refined_deg 0.869 r_scbond_it 0.758 r_chiral_restr 0.049 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.793 r_dihedral_angle_3_deg 13.969 r_dihedral_angle_4_deg 12.667 r_dihedral_angle_1_deg 4.632 r_mcangle_it 2.192 r_mcbond_it 1.175 r_angle_refined_deg 0.869 r_scbond_it 0.758 r_chiral_restr 0.049 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other 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 1313 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing