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Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N8Y Rat ErbB2 extracellular domain (PDB code 1N8Y) and uncomplexed pertuzumab Fab (PDB code 1L7I) experimental model PDB 1L7I Rat ErbB2 extracellular domain (PDB code 1N8Y) and uncomplexed pertuzumab Fab (PDB code 1L7I)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 PEG 3350, ammonium formate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4 69.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.412 α = 90 b = 139.412 β = 90 c = 356.873 γ = 90
Symmetry Space Group P 43 21 2
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 ADSC QUANTUM 4 2001-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.00 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.25 30 99.9 0.116 0.116 19.3 8.2 56393 56351 -3 97.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.25 3.37 100 0.691 0.691 3.3 8.3 5496
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Rat ErbB2 extracellular domain (PDB code 1N8Y) and uncomplexed pertuzumab Fab (PDB code 1L7I) 3.25 15 55651 52816 2835 100 0.2265 0.22655 0.22429 0.26772 0.2807 SHELLS (A): 3.289 - 3.285, 3.370 - 3.366, 3.459 - 3.454, 3.559 - 3.554, 3.670 - 3.664, 3.798 - 3.791, 3.944 - 3.937, 4.117 - 4.107, 4.323 - 4.313, 4.577 - 4.564, 4.904 - 4.886, 5.345 - 5.319, 6.000 - 5.960, 7.157 - 7.073, 10.465 - 10.120 10.586
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] 2.21 2.21 -4.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.52 r_scangle_it 2.83 r_mcangle_it 2.717 r_scbond_it 1.81 r_mcbond_it 1.657 r_angle_refined_deg 1.273 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.52 r_scangle_it 2.83 r_mcangle_it 2.717 r_scbond_it 1.81 r_mcbond_it 1.657 r_angle_refined_deg 1.273 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15302 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 179
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing