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X-ray structure of the intermolecular complex of Clostridium perfringens sortase C with the C-terminal cell wall sorting signal motif.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IXZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 25% (w/v) PEG 3350, 200mM LiSO4, 100mM Tris-HCl, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.83 56.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.21 α = 90 b = 104.21 β = 90 c = 44.87 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2019-12-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.38 18.8 98.6 0.997 11.7 10.5 11342
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.38 2.44 0.909
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 6IXZ 2.38 18.8 11334 541 98.625 0.246 0.2445 0.249 0.2763 0.2775 74.757
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] -0.013 -0.006 -0.013 0.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_dihedral_angle_3_deg 13.824 r_lrange_other 10.665 r_lrange_it 10.661 r_dihedral_angle_4_deg 8.431 r_dihedral_angle_1_deg 8.088 r_mcangle_other 7.147 r_mcangle_it 7.145 r_scangle_it 6.791 r_scangle_other 6.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_dihedral_angle_3_deg 13.824 r_lrange_other 10.665 r_lrange_it 10.661 r_dihedral_angle_4_deg 8.431 r_dihedral_angle_1_deg 8.088 r_mcangle_other 7.147 r_mcangle_it 7.145 r_scangle_it 6.791 r_scangle_other 6.788 r_mcbond_it 4.534 r_mcbond_other 4.508 r_scbond_it 4.346 r_scbond_other 4.344 r_angle_refined_deg 1.5 r_angle_other_deg 1.09 r_nbtor_refined 0.274 r_symmetry_nbtor_other 0.201 r_symmetry_xyhbond_nbd_refined 0.196 r_nbd_refined 0.162 r_nbd_other 0.16 r_symmetry_nbd_other 0.155 r_xyhbond_nbd_refined 0.151 r_symmetry_nbd_refined 0.134 r_chiral_restr 0.051 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1555 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing