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Structure of FabS1CE2_ER-3c in complex with the extracellular region of EGFR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ARU chain A, residues 309-555 experimental model PDB 8TRS fragment representing Hv/Lv of this Fab experimental model PDB 8TRS fragment representing HC1/LC1 of this Fab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.2M potassium thiocyanate, 20% PEG3350, cryoprotected with this buffer plus 30% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.85 68.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.06 α = 90 b = 72.116 β = 101.65 c = 126.211 γ = 90
Symmetry Space Group P 1 21 1
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 mirrors 2025-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979346 NSLS-II 17-ID-2
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 2.4 43.112 95.1 0.13 0.168 0.106 0.988 7.9 4.3 66379 40.33
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 2.4 2.443 100 1.24 1.619 1.029 0.364 1.2 4.5
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 2.4 43.11 1.34 66331 3286 95.07 0.1969 0.1945 0.1947 0.2426 0.2427 58.85
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 17.4106 f_angle_d 1.0545 f_chiral_restr 0.0661 f_bond_d 0.009 f_plane_restr 0.0088
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7883 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 281
Software Software Software Name Purpose PHENIX refinement PHENIX refinement autoPROC data reduction Aimless data scaling PHASER phasing