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Crystal structure of pilus-specific sortase C mutant from Streptococcus sanguinis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8GR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 295 100 mM Sodium Acetate pH 5.5, 200 mM Ammonium sulphate, and 10 % PEG 2000MME.
Crystal Properties Matthews coefficient Solvent content 4.52 69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.455 α = 90 b = 139.455 β = 90 c = 104.692 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 PIXEL DECTRIS PILATUS 6M 2020-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
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 2.008 69.82 93.3 0.088 0.026 0.999 15.9 11.8 24438 42.7
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 2.008 2.043 1.039 0.348 0.871 2.2 9.9
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 8GR6 2.008 69.82 23165 1269 93.33 0.1848 0.1832 0.1944 0.21408 0.2191 RANDOM 54.637
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] -1.89 -0.94 -1.89 6.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.147 r_dihedral_angle_3_deg 12.261 r_long_range_B_other 11.861 r_long_range_B_refined 11.844 r_scangle_other 10.992 r_dihedral_angle_4_deg 9.664 r_scbond_it 9.645 r_scbond_other 9.641 r_mcangle_it 6.68 r_mcangle_other 6.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.147 r_dihedral_angle_3_deg 12.261 r_long_range_B_other 11.861 r_long_range_B_refined 11.844 r_scangle_other 10.992 r_dihedral_angle_4_deg 9.664 r_scbond_it 9.645 r_scbond_other 9.641 r_mcangle_it 6.68 r_mcangle_other 6.68 r_mcbond_it 6.015 r_mcbond_other 5.951 r_dihedral_angle_1_deg 5.585 r_angle_refined_deg 1.068 r_angle_other_deg 0.928 r_chiral_restr 0.058 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1523 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing