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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 2.29 46.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.174 α = 72 b = 42.051 β = 80.28 c = 49.256 γ = 74.19
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 1.4 20 84 0.03 22.8 2.5 48750
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 49.1 5.7
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 1.4 19.12 47402 2494 86.27 0.17188 0.17023 0.1676 0.20281 0.2007 RANDOM 18.01
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] -0.04 0.14 -0.08 0.15 0.15 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.509 r_dihedral_angle_4_deg 14.537 r_dihedral_angle_3_deg 12.781 r_dihedral_angle_1_deg 5.424 r_sphericity_free 5.282 r_sphericity_bonded 4.433 r_scangle_it 4.255 r_scbond_it 3.416 r_mcangle_it 2.471 r_rigid_bond_restr 2.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.509 r_dihedral_angle_4_deg 14.537 r_dihedral_angle_3_deg 12.781 r_dihedral_angle_1_deg 5.424 r_sphericity_free 5.282 r_sphericity_bonded 4.433 r_scangle_it 4.255 r_scbond_it 3.416 r_mcangle_it 2.471 r_rigid_bond_restr 2.374 r_mcbond_it 1.656 r_angle_refined_deg 1.496 r_nbtor_refined 0.307 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.176 r_symmetry_hbond_refined 0.122 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2118 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing