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Crystal structure of the water-soluble FraC purified starting from the trans-membrane pore
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VWI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 Microseeds generated in: 24% PEG 4000, 200 mM ammonium sulfate, 100 mM Cacodylate (pH 7.4)
Single crystals generated in: 8% PEG 4000, 100 mM TRIS-HCl
Crystal Properties Matthews coefficient Solvent content 2.48 50.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.3 α = 90 b = 44.44 β = 92.82 c = 114.95 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 CCD ADSC QUANTUM 315 2014-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 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 2.14 47.19 97.5 0.099 9.7 4.5 42232
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 2.14 2.21 89.3 0.31 3.4 3.8
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 3VWI 2.14 47.19 40061 2118 97.13 0.21269 0.21 0.2172 0.26286 0.2667 RANDOM 18.627
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] -1.34 0.22 0.12 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.006 r_dihedral_angle_3_deg 14.521 r_dihedral_angle_4_deg 13.69 r_dihedral_angle_1_deg 7.306 r_long_range_B_refined 2.887 r_long_range_B_other 2.771 r_angle_refined_deg 1.475 r_scangle_other 0.852 r_angle_other_deg 0.748 r_mcangle_it 0.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.006 r_dihedral_angle_3_deg 14.521 r_dihedral_angle_4_deg 13.69 r_dihedral_angle_1_deg 7.306 r_long_range_B_refined 2.887 r_long_range_B_other 2.771 r_angle_refined_deg 1.475 r_scangle_other 0.852 r_angle_other_deg 0.748 r_mcangle_it 0.642 r_mcangle_other 0.642 r_scbond_it 0.533 r_scbond_other 0.532 r_mcbond_it 0.381 r_mcbond_other 0.38 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5536 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling Aimless phasing