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Crystal Structure of the Grb2 SH2 Domain in Complex with a Cyclopropyl-constrained Ac-pY-Q-N-NH2 Tripeptide Mimic
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HUW pdb entry 2HUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 Ligand in lyophilized powder form was dissolved in a 7.6 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1.7:1. 3.5 uL of this solution was mixed with 3.5 uL of 0.1 M HEPES, 20% w/v PEG MW10,000, pH 7.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after two weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.384 α = 90 b = 63.955 β = 90 c = 92.725 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++ 2007-05-25 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 1.7 50 71.6 0.054 20.4 4.5 27887 19967
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 1.7 1.76 6.6 0.305 1.7 179
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 2HUW 2 50 16854 14090 709 83.6 0.229 0.2249 0.25 0.2459 random 31.558
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] -14.475 7.857 6.618
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.766 c_mcangle_it 2.268 c_scbond_it 1.881 c_angle_d 1.659 c_mcbond_it 1.413 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1643 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 76
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