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Ricin bound to VHH antibody V5E1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AA1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 340 mM ammonium fluoride and 22% PEG 3,350.
Crystal Properties Matthews coefficient Solvent content 3.43 64.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.418 α = 90 b = 161.418 β = 90 c = 67.031 γ = 120
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 RIGAKU SATURN 944 2019-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU R-AXIS 1.54
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 3.049 50 99.9 0.377 0.398 0.126 2.2 9.9 19234 49.64
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 3.05 3.1 100 2.377 2.54 0.88 0.586 8.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2AA1 3.049 34.573 1.35 19213 897 99.92 0.2388 0.237 0.2379 0.2741 0.276 53.1336
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 3.168 f_angle_d 0.543 f_chiral_restr 0.043 f_plane_restr 0.005 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4988 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 99
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction PHASER phasing