☰ Navigation Tabs
Structure of the SHP-2 N-SH2 domain in a 1:2 complex with RVIpYFVPLNR peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AYD PDB entry 1AYD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 20% PEG 3350, 0.1M Bis-Tris, 0.2M Li2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.48 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.865 α = 90 b = 62.865 β = 90 c = 75.322 γ = 90
Symmetry Space Group P 43 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 100 2007-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.98 APS 19-BM
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 1.8 48.3 99.3 0.03 61.5 11.2 15827
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 1.8 1.89 100 0.382 5 11.6
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 PDB entry 1AYD 1.8 32.31 13727 13727 728 99.27 0.19776 0.19679 0.2234 0.21602 0.2313 RANDOM 43.354
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] 0.03 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.781 r_dihedral_angle_4_deg 17.219 r_dihedral_angle_3_deg 15.929 r_dihedral_angle_1_deg 7.397 r_scangle_it 5.397 r_scbond_it 3.376 r_mcangle_it 2.291 r_angle_refined_deg 1.96 r_mcbond_it 1.277 r_chiral_restr 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.781 r_dihedral_angle_4_deg 17.219 r_dihedral_angle_3_deg 15.929 r_dihedral_angle_1_deg 7.397 r_scangle_it 5.397 r_scbond_it 3.376 r_mcangle_it 2.291 r_angle_refined_deg 1.96 r_mcbond_it 1.277 r_chiral_restr 0.146 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 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 911 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling