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Crystal Structure of the Grb2 SH2 Domain in Complex with a 20-Membered Macrocyclic Ligand Having the Sequence pYVNV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 Ligand in lyohpilized power form was dissolved in a 10.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:2. 3.5 uL of this solution was mixed with 3.5 uL of 20% v/v isopropanol, 20% w/v polyethylene glycol MW 4,000, 0.1 M sodium citrate dihydrate, pH 5.6 to create the hanging drop, which yielded crystals of the protein-ligand complex after two weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298KK
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.162 α = 90 b = 83.162 β = 90 c = 96.009 γ = 120
Symmetry Space Group P 32 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 RIGAKU RAXIS IV++ 2006-02-25 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 99.7 0.098 9.9 5.7 25695 25618
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) 2.02 2.09 99.8 0.355 2.4 5.4 2524
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 1JYR 2.02 50 25668 25587 2529 99.7 0.18 0.1786 0.2219 0.1784 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] -0.529 -0.071 -0.529 1.057
RMS Deviations Key Refinement Restraint Deviation c_mcangle_it 2.097 o_mcbond_it 1.335 c_angle_d 1.235 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2571 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling