☰ Navigation Tabs
Crystal Structure of synthetic antibody COP-2 in complex with the C-terminal domain of Clostridium perfringens enterotoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TDM COP-2 and cCpE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 277.15 200 mM sodium chloride, 1.75 M ammonium sulfate, and 100 mM sodium cacodylate pH 6.6
Crystal Properties Matthews coefficient Solvent content 2.91 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.475 α = 90 b = 198.52 β = 109.72 c = 115.8 γ = 90
Symmetry Space Group I 1 2 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 EIGER X 16M 2022-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033167 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.5 29.74 99.1 0.066 0.093 0.066 0.993 6.96 2 81028 45.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.589 98.32 0.535 0.757 0.535 0.506 1.69 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 FREE R-VALUE 2.5 29.74 1.36 80904 3974 99.15 0.1783 0.1807 0.2248 0.2268 Random 55.67
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.494 f_angle_d 1.45 f_chiral_restr 0.072 f_bond_d 0.015 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12804 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling DIALS data reduction PHASER phasing PDB_EXTRACT data extraction