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X-ray structure of Clostridium perfringens pili protein B collagen-binding domains
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 100 mM sodium acetate pH4.8, 400 mM ammonium sulfate, 16-19% w/v PEG400
Crystal Properties Matthews coefficient Solvent content 4.98 81.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.39 α = 90 b = 127.39 β = 90 c = 163.16 γ = 120
Symmetry Space Group P 65 2 2
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 2021-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0 SPring-8 BL45XU
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 2.86 48.83 99.5 0.994 10.13 6.2 18588
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 2.86 2.93 0.704
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.86 48.83 17675 913 99.54 0.25402 0.2524 0.2859 0.2971 RANDOM 92.729
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] 0.45 0.22 0.45 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.584 r_dihedral_angle_3_deg 18.55 r_dihedral_angle_4_deg 16.795 r_long_range_B_refined 10.001 r_long_range_B_other 9.998 r_dihedral_angle_1_deg 8.895 r_scangle_other 6.881 r_mcangle_it 6.438 r_mcangle_other 6.436 r_scbond_it 4.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.584 r_dihedral_angle_3_deg 18.55 r_dihedral_angle_4_deg 16.795 r_long_range_B_refined 10.001 r_long_range_B_other 9.998 r_dihedral_angle_1_deg 8.895 r_scangle_other 6.881 r_mcangle_it 6.438 r_mcangle_other 6.436 r_scbond_it 4.309 r_scbond_other 4.307 r_mcbond_it 4.06 r_mcbond_other 4.036 r_angle_refined_deg 1.673 r_angle_other_deg 1.049 r_chiral_restr 0.058 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_gen_planes_other 0.005 r_bond_other_d 0.004 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 2072 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing