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Ricin A chain bound to VHH antibody V6D4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 295 100 mM MES (pH 6.0), 400 mM zinc acetate, and 11% PEG 8,000
Crystal Properties Matthews coefficient Solvent content 2.79 55.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.937 α = 90 b = 78.605 β = 96.46 c = 103.89 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 2016-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 50 99.7 0.124 0.145 0.076 5.7 3.6 53563
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 2.1 2.14 97.7 1.049 1.248 0.669 0.518 3.2
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.103 46.445 1.35 53533 2606 99.08 0.1907 0.1888 0.1878 0.2275 0.2251 46.35
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] 7.8677 -8.2272 -10.2445 2.3768
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.486 f_angle_d 0.671 f_chiral_restr 0.049 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5867 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 26
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction