☰ Navigation Tabs
HER2 Kinase Domain Complexed with TAK-285
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PP0
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 298K
Crystal Properties Matthews coefficient Solvent content 1.98 37.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.542 α = 90.42 b = 64.936 β = 89.72 c = 92.36 γ = 90.35
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate 2007-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0 APS 23-ID-D
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 3.2 50 76.3 0.083 8.3 1.7 14548
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 3.2 3.31 42.6 0.211 1.5
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 3PP0 3.21 40 13792 749 75.96 0.22729 0.22375 0.2196 0.29352 0.291 RANDOM 51.502
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] -1.03 0.23 -0.03 3.57 0.05 -2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.039 r_dihedral_angle_3_deg 21.263 r_dihedral_angle_4_deg 19.119 r_dihedral_angle_1_deg 5.843 r_angle_refined_deg 1.235 r_scangle_it 0.901 r_mcangle_it 0.801 r_scbond_it 0.493 r_mcbond_it 0.436 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.039 r_dihedral_angle_3_deg 21.263 r_dihedral_angle_4_deg 19.119 r_dihedral_angle_1_deg 5.843 r_angle_refined_deg 1.235 r_scangle_it 0.901 r_mcangle_it 0.801 r_scbond_it 0.493 r_mcbond_it 0.436 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 8860 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 76
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction