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Catalytic domain of human SHP2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B7O PDB ENTRY 3B7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 16-22 % (W/V) PEG3350, 0.1-0.2 M SODIUM CITRATE
Crystal Properties Matthews coefficient Solvent content 2.32 46.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.216 α = 72.52 b = 42.257 β = 81.63 c = 49.197 γ = 74.73
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 MARRESEARCH 2009-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.5 20 86 0.05 17.4 3.2 40770
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 1.5 1.59 51.6 0.02 5.5
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 PDB ENTRY 3B7O 1.5 19.6 40031 2107 85.8 0.18559 0.18413 0.1817 0.21342 0.2119 RANDOM 20.499
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] 0.27 -0.19 0.01 0.34 0.33 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.885 r_dihedral_angle_4_deg 20.591 r_dihedral_angle_3_deg 14.112 r_dihedral_angle_1_deg 6.512 r_scangle_it 5.37 r_scbond_it 3.723 r_mcangle_it 2.344 r_angle_refined_deg 1.862 r_mcbond_it 1.524 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.885 r_dihedral_angle_4_deg 20.591 r_dihedral_angle_3_deg 14.112 r_dihedral_angle_1_deg 6.512 r_scangle_it 5.37 r_scbond_it 3.723 r_mcangle_it 2.344 r_angle_refined_deg 1.862 r_mcbond_it 1.524 r_nbtor_refined 0.311 r_nbd_refined 0.239 r_symmetry_vdw_refined 0.195 r_chiral_restr 0.13 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.116 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2139 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing