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Crystal structure of the extracellular region of rat HER2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M6B PDB entry 1M6B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 15-30% PEG4000, 50mM Na citrate pH5.4, 10mM EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.18 61.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.87 α = 90 b = 116.4 β = 90 c = 55.37 γ = 90
Symmetry Space Group P 21 21 2
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 2001-02-20 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 2.4 20 99.2 5.7 34177 33900 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 93.9 0.77 2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1M6B 2.4 20 1 1 34177 30022 1568 94.39 0.2266 0.2237 0.22375 0.2513 0.28246 0.307 RANDOM 27.924
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] 1.25 -2.57 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.44 r_scangle_it 3.802 r_scbond_it 2.364 r_angle_refined_deg 1.724 r_mcangle_it 1.295 r_mcbond_it 0.675 r_symmetry_vdw_refined 0.274 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.44 r_scangle_it 3.802 r_scbond_it 2.364 r_angle_refined_deg 1.724 r_mcangle_it 1.295 r_mcbond_it 0.675 r_symmetry_vdw_refined 0.274 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.121 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4578 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 70
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement