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Ricin bound to VHH antibody V2C11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AAI 2AAI, 3EZJ experimental model PDB 3EZJ 2AAI, 3EZJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 100 mM Zinc Acetate, 14% PEG 8,000, 22% Glycerol, 80 mM NaCaco pH 6.5, 3% D+Galactose
Crystal Properties Matthews coefficient Solvent content 3.42 64.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.223 α = 90 b = 100.817 β = 90 c = 129.712 γ = 90
Symmetry Space Group P 21 21 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 CCD RIGAKU SATURN 944 2018-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 2.768 50 99.5 0.179 0.198 0.081 4.7 5.5 26051
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 2.77 2.82 95.3 0.816 0.985 0.541 0.685 2.9
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 2AAI, 3EZJ 2.768 32.428 1.35 25976 1339 99.38 0.2095 0.2071 0.2099 0.2545 0.2548 43.3933
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 14.486 f_angle_d 0.599 f_chiral_restr 0.046 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4977 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 155
Software Software Software Name Purpose HKL-2000 data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing