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Phage dUTPases control transfer of virulence genes by a proto- oncogenic G protein-like mechanism.(Staphylococcus bacteriophage 80alpha dUTPase with dUPNHPP).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HQU PDB ENTRY 2HQU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2-6% TERT-BUTANOL, 0.1M TRIS (PH 8.5), 30-50% MPD OR PEG400
Crystal Properties Matthews coefficient Solvent content 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.657 α = 90 b = 88.657 β = 90 c = 88.657 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 CCD ADSC QUANTUM 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.8 44.33 99.9 0.07 23.9 6 5949 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 2.8 2.95 100 0.75 4.7 6.1
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 2HQU 2.8 39.65 5457 477 99.83 0.21999 0.21648 0.2225 0.26362 0.2708 RANDOM 50.523
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] -4.4 4.44 -2.19 8.02 -5.24 -3.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.683 r_dihedral_angle_4_deg 19.736 r_dihedral_angle_3_deg 14.163 r_dihedral_angle_1_deg 3.994 r_mcangle_it 1.074 r_angle_refined_deg 1.021 r_mcbond_it 0.576 r_scbond_it 0.388 r_chiral_restr 0.047 r_bond_refined_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.683 r_dihedral_angle_4_deg 19.736 r_dihedral_angle_3_deg 14.163 r_dihedral_angle_1_deg 3.994 r_mcangle_it 1.074 r_angle_refined_deg 1.021 r_mcbond_it 0.576 r_scbond_it 0.388 r_chiral_restr 0.047 r_bond_refined_d 0.004 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 1309 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing