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The Crystal Structure of the Mutant Nuclease Domain of Pyocin S8 with its Cognate Immunity Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291.15 Sodium Acetate 0.2M, PEG 4000 30%, Tris-HCl 0.1M pH 8.0
Crystal Properties Matthews coefficient Solvent content 1.8 31.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.178 α = 90 b = 47.071 β = 90 c = 99.86 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 80 PIXEL DECTRIS PILATUS 2M 2017-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.458660 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.38 30 89.6 0.038 0.012 1 30.4 9 37296
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.38 1.4 32.1 0.403 0.296 0.795 1.7 1.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4UHP 1.381 29.983 37245 1793 89.413 0.18 0.1781 0.1824 0.212 0.2144 20.364
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] -0.417 -1.337 1.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.207 r_dihedral_angle_4_deg 13.597 r_dihedral_angle_3_deg 12.887 r_rigid_bond_restr 12.356 r_dihedral_angle_1_deg 6.801 r_lrange_it 2.564 r_lrange_other 2.44 r_scangle_it 1.985 r_scangle_other 1.985 r_mcangle_it 1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.207 r_dihedral_angle_4_deg 13.597 r_dihedral_angle_3_deg 12.887 r_rigid_bond_restr 12.356 r_dihedral_angle_1_deg 6.801 r_lrange_it 2.564 r_lrange_other 2.44 r_scangle_it 1.985 r_scangle_other 1.985 r_mcangle_it 1.93 r_mcangle_other 1.929 r_angle_other_deg 1.687 r_scbond_it 1.631 r_scbond_other 1.63 r_mcbond_it 1.58 r_mcbond_other 1.579 r_angle_refined_deg 1.452 r_symmetry_nbd_other 0.213 r_nbd_refined 0.208 r_nbd_other 0.205 r_xyhbond_nbd_other 0.203 r_symmetry_xyhbond_nbd_refined 0.2 r_nbtor_refined 0.188 r_symmetry_nbd_refined 0.174 r_xyhbond_nbd_refined 0.126 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.063 r_bond_other_d 0.018 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing