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HER2 extracelluar region with affinity matured 3-helix affibody ZHER2:342
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S78 1S78 and 1LP1 experimental model PDB 1LP1 1S78 and 1LP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 279 0.05M sodium chloride, 7.5% PEG3350, 0.1M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 3.45 64.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.726 α = 90 b = 97.841 β = 90 c = 148.283 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 115 CCD MARMOSAIC 325 mm CCD 2008-08-07 M SINGLE WAVELENGTH 2 1 x-ray 115 CCD MARMOSAIC 225 mm CCD 2008-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.98 SSRL BL11-1 2 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87 ESRF ID23-2
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 2.9 40 96.7 0.09 13 3.9 22414 21673 -5 -2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1S78 and 1LP1 2.9 40 21673 21673 1333 96.69 0.20804 0.20397 0.27756 0.2324 RANDOM 53.182
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] -1.23 1.66 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.717 r_dihedral_angle_4_deg 20.722 r_dihedral_angle_3_deg 19.539 r_dihedral_angle_1_deg 6.389 r_scangle_it 4.903 r_mcangle_it 4.858 r_scbond_it 3.117 r_mcbond_it 2.985 r_angle_refined_deg 1.359 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.717 r_dihedral_angle_4_deg 20.722 r_dihedral_angle_3_deg 19.539 r_dihedral_angle_1_deg 6.389 r_scangle_it 4.903 r_mcangle_it 4.858 r_scbond_it 3.117 r_mcbond_it 2.985 r_angle_refined_deg 1.359 r_nbtor_refined 0.311 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.092 r_symmetry_hbond_refined 0.034 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 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 4817 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 56
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XDS data scaling