☰ Navigation Tabs
Fc fragment of IgG1 (Herceptin) with protein-A mimetic peptide dendrimer ligand.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HZH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 10-20% PEG 20K, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.88 57.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.778 α = 90 b = 79.155 β = 90 c = 139.223 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 100 CCD MAR CCD 165 mm SI[111] horizontally focussing monochromator 2006-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8162 EMBL/DESY, HAMBURG X11
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 2.3 40 99.3 0.064 35.7 10.8 25671 25480 56.5
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 2.3 2.38 97.5 0.599 2.37 5.3 2442
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 1HZH 2.3 40 25805 24234 806 99.31 0.19025 0.18811 0.2027 0.25716 0.2673 RANDOM 72.418
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] -2.17 0.2 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.544 r_dihedral_angle_4_deg 18.307 r_dihedral_angle_3_deg 16.405 r_dihedral_angle_1_deg 6.687 r_scangle_it 2.743 r_scbond_it 1.894 r_angle_refined_deg 1.86 r_mcangle_it 1.141 r_mcbond_it 0.81 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.544 r_dihedral_angle_4_deg 18.307 r_dihedral_angle_3_deg 16.405 r_dihedral_angle_1_deg 6.687 r_scangle_it 2.743 r_scbond_it 1.894 r_angle_refined_deg 1.86 r_mcangle_it 1.141 r_mcbond_it 0.81 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.198 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.101 r_bond_refined_d 0.021 r_gen_planes_refined 0.006 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 3343 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 350
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing