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Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.22 44.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.223 α = 90 b = 141.32 β = 89.99 c = 62.452 γ = 90
Symmetry Space Group C 1 2 1
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 MAR scanner 345 mm plate 2007-07-11 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 1.69 50 91.3 0.066 24.5 5.8 80867 73832
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) 1.69 1.75 69.4 0.275 3.7 4.1 7850
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 2HUW 2 50 48588 45980 2376 94.6 0.1803 0.1804 0.2233 0.1666 random
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] 2.396 0.138 -2.535
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5505 Nucleic Acid Atoms Solvent Atoms 728 Heterogen Atoms 45
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling