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Structures of TcdB in complex with R-Ras
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OQ7 6OQ7,2FN4 experimental model PDB 2FN4 6OQ7,2FN4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2M ammonium acetate, 0.1M sodium citrate tribasic dihydrate, pH 4.8, and 17% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.62 52.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.308 α = 90 b = 112.112 β = 95.89 c = 101.571 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 EIGER2 X 16M 2020-12-11 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 2.34 112.11 98.9 0.085 0.993 9.6 3.4 70923
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 2.34 2.39 0.693
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 6OQ7,2FN4 2.34 76.02 67379 3516 98.8 0.203 0.201 0.2 0.241 0.2403 RANDOM 37.61
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 1.94 -2.03 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.115 r_dihedral_angle_4_deg 20.044 r_dihedral_angle_3_deg 17.422 r_dihedral_angle_1_deg 6.181 r_long_range_B_refined 3.827 r_long_range_B_other 3.804 r_scangle_other 2.5 r_mcangle_it 2.17 r_mcangle_other 2.17 r_scbond_other 1.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.115 r_dihedral_angle_4_deg 20.044 r_dihedral_angle_3_deg 17.422 r_dihedral_angle_1_deg 6.181 r_long_range_B_refined 3.827 r_long_range_B_other 3.804 r_scangle_other 2.5 r_mcangle_it 2.17 r_mcangle_other 2.17 r_scbond_other 1.538 r_scbond_it 1.537 r_angle_other_deg 1.459 r_mcbond_it 1.306 r_mcbond_other 1.306 r_angle_refined_deg 1.23 r_chiral_restr 0.062 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 11614 Nucleic Acid Atoms Solvent Atoms 539 Heterogen Atoms 265
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing