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Crystal structure of the full-length Human Protein Tyrosine Phosphatase SHP-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B3O pdb entry 2B3O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 278 2.5 ul of SHP-1 at 3.5 mg/ml in 25mM Tris-HCl, beta-mercaptoethanol, 1mM EDTA mixed with 2.5 ul of 1.8M ammonium sulfate, 0.1M glycine, 0.1M Tris-HCl, with the addition of 0.5 ul 14mM deoxy Big Chap to form the final drop., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 3.02 59.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 231.919 α = 90 b = 231.919 β = 90 c = 78.852 γ = 120
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 MAR CCD 165 mm 2007-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CAMD BEAMLINE GCPCC 1.3807 CAMD GCPCC
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 3.1 116 99.9 0.086 18.1 14036 1.5 1.5
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 3.1 3.21 98.5 0.596 1.5
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 2B3O 3.1 115.96 14036 731 99.75 0.2272 0.22481 0.218 0.27576 0.2679 RANDOM 82.953
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] -0.26 -0.13 -0.26 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.494 r_dihedral_angle_3_deg 15.175 r_dihedral_angle_4_deg 14.357 r_dihedral_angle_1_deg 4.343 r_angle_refined_deg 0.855 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4224 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 25
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling