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X-ray structure of Clostridium perfringens pili protein B N-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8GSX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 50 mM bis-tris pH 6.5, 50 mM ammonium sulfate, 30% v/v pentaerythritol ethoxylate (15/4 EO/OH)
Crystal Properties Matthews coefficient Solvent content 1.96 37.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.08 α = 90 b = 39.08 β = 90 c = 290.59 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 PIXEL DECTRIS PILATUS3 6M 2022-03-22 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 1.55 48.48 99.98 0.999 23.23 9.4 39168
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 1.55 1.59 0.789
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 8GSX 1.55 48.48 37233 1935 99.98 0.1868 0.18393 0.1939 0.23963 0.2412 RANDOM 31.172
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 0.07 0.13 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.922 r_dihedral_angle_4_deg 20.025 r_dihedral_angle_3_deg 13.58 r_dihedral_angle_1_deg 7.874 r_rigid_bond_restr 6.258 r_long_range_B_refined 5.806 r_long_range_B_other 5.804 r_scangle_other 5.594 r_scbond_it 4.877 r_scbond_other 4.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.922 r_dihedral_angle_4_deg 20.025 r_dihedral_angle_3_deg 13.58 r_dihedral_angle_1_deg 7.874 r_rigid_bond_restr 6.258 r_long_range_B_refined 5.806 r_long_range_B_other 5.804 r_scangle_other 5.594 r_scbond_it 4.877 r_scbond_other 4.877 r_mcangle_it 4.274 r_mcangle_other 4.273 r_mcbond_it 3.543 r_mcbond_other 3.541 r_angle_refined_deg 1.502 r_angle_other_deg 1.344 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 1988 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing