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X-ray structure of Clostridium perfringens pili CppB-D3D4D5-CppA covalent complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2 M Magnesium formate dihydrate, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.72 54.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.36 α = 93.63 b = 70.71 β = 107.2 c = 110.59 γ = 89.9
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 2024-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.85 48.36 95.6 0.996 8.98 1.8 156433
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 1.85 1.9 0.854
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 AlphaFold 1.85 48.36 148531 7902 95.62 0.19058 0.18923 0.196 0.21619 0.2209 RANDOM 29.952
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] -0.13 -0.15 -0.14 -0.24 -0.18 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.402 r_dihedral_angle_1_deg 9.6 r_long_range_B_refined 8.421 r_long_range_B_other 8.347 r_dihedral_angle_2_deg 7.239 r_scangle_other 6.483 r_scbond_it 4.386 r_scbond_other 4.386 r_mcangle_it 3.823 r_mcangle_other 3.823
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.402 r_dihedral_angle_1_deg 9.6 r_long_range_B_refined 8.421 r_long_range_B_other 8.347 r_dihedral_angle_2_deg 7.239 r_scangle_other 6.483 r_scbond_it 4.386 r_scbond_other 4.386 r_mcangle_it 3.823 r_mcangle_other 3.823 r_mcbond_it 2.883 r_mcbond_other 2.883 r_angle_refined_deg 0.5 r_angle_other_deg 0.215 r_chiral_restr 0.027 r_bond_refined_d 0.001 r_bond_other_d r_dihedral_angle_4_deg r_gen_planes_refined r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12506 Nucleic Acid Atoms Solvent Atoms 1565 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing