☰ Navigation Tabs
Structures of TcdB in complex with Cdc42
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BVM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M sodium cacodylate (pH 6.6), 2.4 M ammonium sulfate, and 2.5% (v/v) Jeffamine M-600 (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.91 57.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.354 α = 90 b = 140.948 β = 90 c = 111.803 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER X 16M 2018-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.79 111.8 100 0.063 0.999 16.9 6.7 24433
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 2.79 2.94 0.865 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 2BVM 2.79 92.4 23173 1241 99.93 0.21666 0.21437 0.2178 0.25924 0.2583 RANDOM 77.173
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] -1.82 4.68 -2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.721 r_dihedral_angle_4_deg 15.1 r_dihedral_angle_3_deg 14.801 r_long_range_B_other 9.517 r_long_range_B_refined 9.514 r_mcangle_other 6.996 r_mcangle_it 6.994 r_scangle_other 6.46 r_dihedral_angle_1_deg 6.35 r_mcbond_it 4.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.721 r_dihedral_angle_4_deg 15.1 r_dihedral_angle_3_deg 14.801 r_long_range_B_other 9.517 r_long_range_B_refined 9.514 r_mcangle_other 6.996 r_mcangle_it 6.994 r_scangle_other 6.46 r_dihedral_angle_1_deg 6.35 r_mcbond_it 4.524 r_mcbond_other 4.512 r_scbond_it 4.198 r_scbond_other 4.124 r_angle_refined_deg 1.31 r_angle_other_deg 1.159 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 5787 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing