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Crystallographic trimer of HER2 extracellular regions in complex with tryptophan-rich antibody fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S78 1S78 chain A, 1FVD chains A,B experimental model PDB 1FVD 1S78 chain A, 1FVD chains A,B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 293 NaCl, Na/K-phosphate, Li-sulfate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.22 α = 90 b = 182.22 β = 90 c = 330.851 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 210 2007-07-10 M SINGLE WAVELENGTH 2 1 x-ray 110 CCD ADSC QUANTUM 315 2007-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 .98 ALS 5.0.1 2 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1,2 3.2 50 96.2 0.147 13 8.3 52459
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1S78 chain A, 1FVD chains A,B 3.2 50 50562 1636 96.35 0.20689 0.20615 0.2053 0.22989 0.2286 RANDOM 71.724
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] 4.23 2.12 4.23 -6.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.728 r_dihedral_angle_4_deg 15.628 r_dihedral_angle_3_deg 15.513 r_dihedral_angle_1_deg 5.755 r_mcangle_it 3.192 r_scangle_it 2.946 r_mcbond_it 1.849 r_scbond_it 1.848 r_angle_refined_deg 1.096 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.728 r_dihedral_angle_4_deg 15.628 r_dihedral_angle_3_deg 15.513 r_dihedral_angle_1_deg 5.755 r_mcangle_it 3.192 r_scangle_it 2.946 r_mcbond_it 1.849 r_scbond_it 1.848 r_angle_refined_deg 1.096 r_nbtor_refined 0.303 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.134 r_xyhbond_nbd_refined 0.105 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 7920 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 169
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling