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Crystal structure of the human tyrosine phosphatase SHP2 (PTPN11) with an accessible active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2SHP PDB entry 2SHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% PEG 3350, 0.15 M Na Malate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.813 α = 90 b = 86.496 β = 90 c = 166.555 γ = 90
Symmetry Space Group C 2 2 21
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 MARMOSAIC 225 mm CCD 2007-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00721 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 34.12 99.9 0.092 0.092 13.3 4.1 43184 43184 19.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 100 1.01 1.01 2 4 25196
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 (All) 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 2SHP 1.6 34.12 40383 40383 2157 98.35 0.17204 0.17204 0.17009 0.1785 0.20897 0.2118 RANDOM 16.903
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] 0.43 -0.41 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.548 r_dihedral_angle_4_deg 18.865 r_dihedral_angle_3_deg 13.139 r_dihedral_angle_1_deg 5.385 r_scangle_it 4.455 r_scbond_it 3.025 r_mcangle_it 1.896 r_angle_refined_deg 1.593 r_mcbond_it 1.407 r_angle_other_deg 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.548 r_dihedral_angle_4_deg 18.865 r_dihedral_angle_3_deg 13.139 r_dihedral_angle_1_deg 5.385 r_scangle_it 4.455 r_scbond_it 3.025 r_mcangle_it 1.896 r_angle_refined_deg 1.593 r_mcbond_it 1.407 r_angle_other_deg 0.96 r_mcbond_other 0.349 r_symmetry_vdw_other 0.334 r_nbd_refined 0.215 r_nbd_other 0.202 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.133 r_symmetry_vdw_refined 0.108 r_chiral_restr 0.097 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2185 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling PHASER phasing