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X-ray structure of Clostridium perfringens sortase C with the C-terminal cell wall sorting 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 298 30% (w/v) PEG 4000, 200mM LiSO4, 100mM Tris-HCl, pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.99 38.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.23 α = 90 b = 62.69 β = 102.58 c = 77.69 γ = 90
Symmetry Space Group C 1 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++ 2019-10-09 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 1.68 19.02 97.6 0.998 12.56 2.4 43526
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 1.68 1.72 0.839
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 6IXZ 1.68 19.02 41328 2197 97.67 0.15873 0.1554 0.1662 0.22033 0.2295 RANDOM 28.313
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] 0.09 -0.02 -0.17 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.912 r_dihedral_angle_3_deg 12.661 r_dihedral_angle_4_deg 10.395 r_dihedral_angle_1_deg 7.378 r_scangle_other 6.07 r_long_range_B_refined 5.872 r_long_range_B_other 5.852 r_rigid_bond_restr 5.572 r_scbond_it 5.316 r_scbond_other 5.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.912 r_dihedral_angle_3_deg 12.661 r_dihedral_angle_4_deg 10.395 r_dihedral_angle_1_deg 7.378 r_scangle_other 6.07 r_long_range_B_refined 5.872 r_long_range_B_other 5.852 r_rigid_bond_restr 5.572 r_scbond_it 5.316 r_scbond_other 5.314 r_mcangle_it 4.598 r_mcangle_other 4.597 r_mcbond_it 3.944 r_mcbond_other 3.853 r_angle_refined_deg 1.535 r_angle_other_deg 1.313 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2966 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing