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Crystal Structure of the Kinase domain of Human HER2 (erbB2).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 20% PEG 3550, 200mM di-Ammonium Tartrate, 100 mM PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.92 35.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.705 α = 90 b = 78.951 β = 90 c = 152.675 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 ADSC QUANTUM 315 2005-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.0 ALS 5.0.3
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 2.25 50 99.5 0.08 15.1 3.9 28773
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 2.25 2.33 96.6 0.553 1.82 3.6
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 1M14 2.25 50 27014 1438 99.16 0.18865 0.18484 0.1855 0.26035 0.2591 RANDOM 42.366
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] 3.38 -0.5 -2.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.178 r_dihedral_angle_4_deg 17.091 r_dihedral_angle_3_deg 16.61 r_scangle_it 7.862 r_dihedral_angle_1_deg 5.949 r_scbond_it 5.467 r_mcangle_it 3.36 r_mcbond_it 2.012 r_angle_refined_deg 1.27 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.178 r_dihedral_angle_4_deg 17.091 r_dihedral_angle_3_deg 16.61 r_scangle_it 7.862 r_dihedral_angle_1_deg 5.949 r_scbond_it 5.467 r_mcangle_it 3.36 r_mcbond_it 2.012 r_angle_refined_deg 1.27 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 4657 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 68
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling