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Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-E-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 lyophilized powder form was dissolved in a 9.5 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 4uL of this solution was mixed with 3uL of 0.1 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 1.73 29.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.873 α = 90 b = 41.873 β = 90 c = 108.811 γ = 90
Symmetry Space Group P 43 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 100 IMAGE PLATE RIGAKU RAXIS IV 2007-04-21 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 2.02 50 98.4 0.05 63.8 8.8 6925 6814
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 2.02 2.09 100 0.102 9 669
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 2.02 50 7067 6723 350 95.1 0.1975 0.2029 0.2296 0.2042 random 16.3393
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] 0.866 0.866 -1.732
RMS Deviations Key Refinement Restraint Deviation c_angle_d 1.622 c_mcangle_it 1.62 c_mcbond_it 1.114 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 824 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 41
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling