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Crystal structure of a llama VHH antibody BCD090-M2 against human ErbB3 in space group P1 with cadmium ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EZW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 Protein solution:
17 mg/ml in 20 mM HEPES pH 7.5, 50 mM NaCl
Reservoir solution:
0.1 M MES pH 6.5, 12% w/v PEG 3350, 5 mM CdSO4
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.766 α = 89.992 b = 41.526 β = 67.921 c = 46.487 γ = 76.062
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293.15 CCD APEX II CCD 2017-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS MICROFOCUS 1.54184
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 1.90000753152 32.3416437838 100 0.144282201545 0.15 0.0395 0.997 12.9301230207 13.0920515404 18859 15.2376005709
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.90000753152 1.93276488574 0.833387206263 1.56474169635 4.79135135135
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 FREE R-VALUE 6EZW 1.90000753152 32.3416437838 0.119369942261 18248 1829 96.765298547 0.178155788177 0.17376345673 0.1742 0.217608275476 0.2173 19.8620885272
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 20.0180771652 f_angle_d 1.53085536185 f_chiral_restr 0.072200302117 f_bond_d 0.0139147074203 f_plane_restr 0.0082941237946
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1962 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 2
Software Software Software Name Purpose APEX 2 data collection SAINT data reduction SADABS data scaling PHASER phasing PHENIX model building Coot model building PHENIX refinement