☰ Navigation Tabs
Crystal structure the Fab fragment of matuzumab (Fab72000) in complex with domain III of the extracellular region of EGFR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YY9 1YY9, 3C08 experimental model PDB 3C08 1YY9, 3C08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 298 16% PEG 3350, 1M NaCl, pH 6.0, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.68 66.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.073 α = 90 b = 205.035 β = 117.49 c = 81.577 γ = 90
Symmetry Space Group C 1 2 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 CCD MAR CCD 130 mm M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.2 50 99.7 0.118 8.3 3.5 33886 33886
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 3.2 3.31 98.7 0.354 3.2 3339
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 THROUGHOUT 1YY9, 3C08 3.2 36.56 33738 32028 1708 99.73 0.245 0.242 0.2402 0.299 0.2992 RANDOM 47.909
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] 0.79 0.21 -0.38 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.604 r_dihedral_angle_3_deg 19.885 r_dihedral_angle_4_deg 16.97 r_dihedral_angle_1_deg 7.04 r_angle_refined_deg 1.333 r_scangle_it 1.229 r_mcangle_it 0.797 r_scbond_it 0.729 r_mcbond_it 0.432 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.604 r_dihedral_angle_3_deg 19.885 r_dihedral_angle_4_deg 16.97 r_dihedral_angle_1_deg 7.04 r_angle_refined_deg 1.333 r_scangle_it 1.229 r_mcangle_it 0.797 r_scbond_it 0.729 r_mcbond_it 0.432 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.303 r_nbd_refined 0.255 r_xyhbond_nbd_refined 0.164 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8359 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 173
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction