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Structure of TcdA GTD in complex with RhoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FTN 1FTN, 3SRZ experimental model PDB 3SRZ 1FTN, 3SRZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2 M Ammonium sulfate, 0.1 M MES, pH 5.9, and 10% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.68 54.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.641 α = 90 b = 122.798 β = 90 c = 127.474 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 2021-03-31 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 2.596 83.799 98.5 0.1 0.997 10.79 3.8 27633
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 0.902 0.587
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1FTN, 3SRZ 2.596 83.799 27633 1276 98.146 0.216 0.2149 0.2159 0.2354 0.2357 60.029
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] 4.628 -3.849 -0.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.236 r_dihedral_angle_4_deg 23.197 r_dihedral_angle_3_deg 18.466 r_lrange_it 7.562 r_scangle_it 5.514 r_dihedral_angle_1_deg 5.112 r_mcangle_it 4.849 r_scbond_it 3.813 r_mcbond_it 3.156 r_angle_refined_deg 1.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.236 r_dihedral_angle_4_deg 23.197 r_dihedral_angle_3_deg 18.466 r_lrange_it 7.562 r_scangle_it 5.514 r_dihedral_angle_1_deg 5.112 r_mcangle_it 4.849 r_scbond_it 3.813 r_mcbond_it 3.156 r_angle_refined_deg 1.109 r_symmetry_nbd_refined 0.347 r_nbtor_refined 0.318 r_symmetry_xyhbond_nbd_refined 0.288 r_xyhbond_nbd_refined 0.222 r_nbd_refined 0.215 r_chiral_restr 0.089 r_metal_ion_refined 0.086 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5810 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 71
Software Software Software Name Purpose XDS data reduction XDS data scaling PHENIX phasing REFMAC refinement