☰ Navigation Tabs
Crystal structure of Trastuzumab Fc conjugated to Linker-Payload
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1 M MES, pH 6.5, 5% v/v MPD, 15% w/v PEG6000
Crystal Properties Matthews coefficient Solvent content 2.83 56.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.458 α = 90 b = 79.59 β = 90 c = 138.112 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 PIXEL DECTRIS PILATUS 6M Collimating Mirror with two stripes (Si, Rh/Pt); Toroidal Focusing Mirror (Rh/Pt) 2024-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.180530 CLSI 08B1-1
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 2.46 68.96 93.4 0.119 0.122 0.034 0.999 15.8 12.9 15166 62.57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.46 2.66 2.118 2.217 0.645
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 2.46 68.96 1.34 15162 767 74.07 0.25 0.2488 0.2475 0.272 0.2699 69.05
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 12.5843 f_angle_d 0.5134 f_chiral_restr 0.0416 f_plane_restr 0.0039 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3267 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 244
Software Software Software Name Purpose autoPROC data processing XDS data reduction STARANISO data scaling pointless data scaling Aimless data scaling PHENIX refinement Coot model building