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High-resolution structure of vWF A1 domain in complex with caplacizumab, the first nanobody-based medicine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293.15 20 mM Tris-HCl pH 8
150 mM NaCl
10% glycerol
40% glycerol ethoxylate
Crystal Properties Matthews coefficient Solvent content 2.37 48.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.741 α = 90 b = 74.741 β = 90 c = 122.288 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 PIXEL DECTRIS EIGER X 9M 2019-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.6 27.55 95.37 0.064 0.996 5.36 5 48735 20.22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 0.541 0.943 5.36 10.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5GGS 1.6 27.55 1.36 48735 2373 95.37 0.1765 0.1754 0.1765 0.1984 0.201 4.87% 29.81
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 3.0079 f_angle_d 0.8007 f_chiral_restr 0.0517 f_bond_d 0.0059 f_plane_restr 0.0049
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2600 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms
Software Software Software Name Purpose MxDC data collection PHENIX refinement HKL-2000 data scaling PHENIX model building MOLREP phasing