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TLT-1 binding Fab of the bispecific antibody HMB-001 in complex with the TLT-1 stalk peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KMV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 291 1M lithium chloride, 20% (w/v) PEG 6000, 100 mM citric acid/NaOH, pH 4.0
Crystal Properties Matthews coefficient Solvent content 2.28 46.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.234 α = 91.88 b = 65.377 β = 91.72 c = 67.145 γ = 92.89
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 16M 2018-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.98 MAX IV BioMAX
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 1.49 28.46 91.03 0.05225 0.07387 0.05222 0.994 9.03 1.9 140068 18.72
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 1.49 1.543 62.1 0.5929 0.8384 0.5928 0.0678 1.37 1.9
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 FREE R-VALUE 1.49 28.46 2 134358 1783 91.05 0.1572 0.157 0.1562 0.174 0.1737 24.02
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 6.1506 f_angle_d 0.9548 f_chiral_restr 0.0814 f_bond_d 0.0087 f_plane_restr 0.0081
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6814 Nucleic Acid Atoms Solvent Atoms 1019 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing