☰ Navigation Tabs
Structure of SHP2 N-SH2 domain in complex with RLNpYAQLWHR 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, 0.1 M bis-Tris, 0.2 M Li2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.7 54.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.749 α = 90 b = 62.749 β = 90 c = 75.323 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 CCD 2001-03-05 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 2.05 48.2 99 0.064 46.5 10.9 9943
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 2.05 2.13 100 0.364 6.7 11.3
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 PDB entry 1AYD 2.05 24.11 9354 467 98.77 0.19448 0.1927 0.2081 0.23358 0.2484 RANDOM 44.269
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] -0.29 -0.29 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.603 r_dihedral_angle_3_deg 16.194 r_dihedral_angle_4_deg 13.902 r_dihedral_angle_1_deg 6.593 r_scangle_it 5.982 r_scbond_it 3.777 r_mcangle_it 2.721 r_angle_refined_deg 2.096 r_mcbond_it 1.525 r_chiral_restr 0.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.603 r_dihedral_angle_3_deg 16.194 r_dihedral_angle_4_deg 13.902 r_dihedral_angle_1_deg 6.593 r_scangle_it 5.982 r_scbond_it 3.777 r_mcangle_it 2.721 r_angle_refined_deg 2.096 r_mcbond_it 1.525 r_chiral_restr 0.166 r_bond_refined_d 0.025 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 831 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 5
Software Software Software Name Purpose MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling