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X-ray structure of Clostridium perfringens pili protein CppA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XCB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M Sodium formate, 0.1M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Sodium potassium tartrate tetrahydrate, 0.1M Sodium oxamate, 0.1M Imidazole, o.1M MES monohydrate (acid), 20% v/v Ethylene glycol, 10% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.47 50.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.34 α = 90 b = 71.33 β = 90 c = 228.76 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2016-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 2.48 114.38 99.4 0.068 16.08 5.28 37465
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 2.48 2.54 98.6 0.49 3.71
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5XCB 2.48 114.38 35598 1867 99.37 0.22974 0.2275 0.27182 0.2687 RANDOM 46.56
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] 0.02 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.312 r_dihedral_angle_3_deg 11.665 r_dihedral_angle_4_deg 5.65 r_dihedral_angle_1_deg 5.323 r_long_range_B_refined 3.359 r_long_range_B_other 3.341 r_mcangle_it 1.907 r_mcangle_other 1.907 r_scangle_other 1.786 r_mcbond_it 1.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.312 r_dihedral_angle_3_deg 11.665 r_dihedral_angle_4_deg 5.65 r_dihedral_angle_1_deg 5.323 r_long_range_B_refined 3.359 r_long_range_B_other 3.341 r_mcangle_it 1.907 r_mcangle_other 1.907 r_scangle_other 1.786 r_mcbond_it 1.111 r_mcbond_other 1.111 r_scbond_it 1.046 r_scbond_other 1.046 r_angle_refined_deg 0.757 r_angle_other_deg 0.544 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 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 7018 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing