☰ Navigation Tabs
Crystal structure of extracellular domain of human HER2 complexed with Herceptin Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M6B PDB 1M6B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 20-30% PEG 5000 MME, 0.1M MES pH6.5, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.89 57.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.17 α = 90 b = 109.77 β = 90 c = 175.14 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 110 CCD ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 20 96.4 3.9 44400 42223 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.52 2.58 90
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 PDB 1M6B 2.52 20 1 1 42223 37518 1871 92.88 0.226 0.22521 0.22205 0.28425 0.2937 RANDOM 16.813
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] -2.69 -0.37 3.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.713 r_scangle_it 3.61 r_scbond_it 2.193 r_angle_refined_deg 1.786 r_mcangle_it 1.283 r_mcbond_it 0.654 r_symmetry_vdw_refined 0.28 r_nbd_refined 0.248 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.713 r_scangle_it 3.61 r_scbond_it 2.193 r_angle_refined_deg 1.786 r_mcangle_it 1.283 r_mcbond_it 0.654 r_symmetry_vdw_refined 0.28 r_nbd_refined 0.248 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.111 r_symmetry_hbond_refined 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7778 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 33
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement