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Crystal Structure of Src SH2 domain bound to doubly phosphorylated peptide PQpYIpYVPA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SPS PDB entry 1sps
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 296 PEG 4000, magnesium chloride,Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 1.97 37.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.256 α = 90 b = 67.727 β = 90 c = 29.636 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 30 90.4 0.101 14206 1 2 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 1sps 2.1 29.64 2 1 11148 10857 1128 87.5 0.224 0.2343 0.271 0.2429 RANDOM 16.8
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] -2.46 1.16 1.3
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.2 c_scangle_it 2.36 c_mcangle_it 1.89 c_scbond_it 1.66 c_angle_deg 1.4 c_mcbond_it 1.18 c_improper_angle_d 0.89 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1675 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 13
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing