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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 2.31 46.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.19 α = 71.99 b = 42.091 β = 81.09 c = 49.386 γ = 75.36
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 83 0.04 13.8 2.5 39749
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 50.7 0.04 3.4
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 19.53 39569 2126 87.76 0.19249 0.19056 0.1898 0.22747 0.2259 RANDOM 14.745
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] 1.14 -0.14 -0.22 -0.52 0.45 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.987 r_dihedral_angle_4_deg 17.027 r_dihedral_angle_3_deg 15.248 r_dihedral_angle_1_deg 6.133 r_scangle_it 5.058 r_scbond_it 3.65 r_mcangle_it 2.126 r_angle_refined_deg 2.012 r_mcbond_it 1.549 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.987 r_dihedral_angle_4_deg 17.027 r_dihedral_angle_3_deg 15.248 r_dihedral_angle_1_deg 6.133 r_scangle_it 5.058 r_scbond_it 3.65 r_mcangle_it 2.126 r_angle_refined_deg 2.012 r_mcbond_it 1.549 r_nbtor_refined 0.316 r_nbd_refined 0.245 r_symmetry_vdw_refined 0.242 r_chiral_restr 0.152 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.092 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 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 2185 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing