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X-ray structure of major pilin from C. perfringens SM101
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XCC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 298 4% v/v Tacsimate buffer pH 4.0 (73mM malonic acid, 10mM ammonium citrate tribasic, 5mM succinic acid, 12mM D,L-malic acid, 16mM sodium acetate trihydrate, 20mM sodium formate, 6.4mM ammonium tartrate dibasic), 12% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.14 60.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.14 α = 90 b = 111.83 β = 107.79 c = 118.59 γ = 90
Symmetry Space Group P 1 21 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 2M 2018-06-17 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) R Merge I (Observed) 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 2.72 48.71 99.1 0.085 13.8 3.4 69104
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.72 2.79 0.495 2.9
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 5XCC 2.72 48.71 65602 3502 99.17 0.22977 0.22728 0.2306 0.27554 0.2748 RANDOM 45.106
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] -0.18 0.21 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.372 r_dihedral_angle_3_deg 18.217 r_dihedral_angle_1_deg 10.517 r_dihedral_angle_4_deg 8.604 r_angle_refined_deg 1.022 r_angle_other_deg 0.776 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.372 r_dihedral_angle_3_deg 18.217 r_dihedral_angle_1_deg 10.517 r_dihedral_angle_4_deg 8.604 r_angle_refined_deg 1.022 r_angle_other_deg 0.776 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13922 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing