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Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-Q-N-NH2 Tripeptide Mimic
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C7I pdb entry 3C7I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 Ligand in lyphilized powder form was dissolved in a 9.1 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 3 uL of this solution was mixed with 4 uL of 0.2 M MgCl2 x 6H2O, 30% w/v PEG MW4000, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.789 31.262
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.239 α = 90 b = 42.243 β = 90 c = 110.384 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE RIGAKU RAXIS IV 2007-03-01 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 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 1.79 50 94.7 0.049 50.8 5.9 19302 18279
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 1.79 1.85 96.1 0.084 5.9 1797
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-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 3C7I 2 50 13945 12970 641 93 0.199 0.2073 0.237 0.2079 random 11.313
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] 0.005 0.049 -0.055
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.528 c_scbond_it 1.776 c_mcangle_it 1.663 c_angle_d 1.544 c_mcbond_it 1.114 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1664 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 81
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing CNS refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling