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Crystal Structure of pilus-specific Sortase C from Streptococcus sanguinis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D7W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 100mM Sodium acetate (pH 5.5), 200mM Ammonium-Sulphate and 10% (w/v) PEG 2000 MME and 12.5 mM Zinc-Chloride
Crystal Properties Matthews coefficient Solvent content 4.05 69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.019 α = 90 b = 140.019 β = 90 c = 103.625 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 PILATUS3 2M 2021-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.056 52.331 97.2 0.06 0.065 0.024 0.999 13.7 6.6 23670
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.056 2.092 100 0.58 0.625 0.23 0.91 2.4 7.1
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 4D7W 2.06 52.33 22519 1150 97.21 0.1795 0.17847 0.1884 0.19868 0.2091 RANDOM 56.162
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] -1.18 -0.59 -1.18 3.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.594 r_dihedral_angle_3_deg 13.247 r_dihedral_angle_4_deg 9.251 r_long_range_B_refined 8.132 r_long_range_B_other 8.131 r_dihedral_angle_1_deg 6.801 r_scangle_other 5.735 r_scbond_it 4.226 r_scbond_other 4.224 r_mcangle_it 3.605
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.594 r_dihedral_angle_3_deg 13.247 r_dihedral_angle_4_deg 9.251 r_long_range_B_refined 8.132 r_long_range_B_other 8.131 r_dihedral_angle_1_deg 6.801 r_scangle_other 5.735 r_scbond_it 4.226 r_scbond_other 4.224 r_mcangle_it 3.605 r_mcangle_other 3.604 r_mcbond_it 2.608 r_mcbond_other 2.6 r_angle_refined_deg 1.438 r_angle_other_deg 1.069 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1534 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing