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Crystal Structure of the Grb2 SH2 Domain in Complex with a Tripeptide: Ac-pY-Ac6c-N-isohexyl
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 An aqueous solution containing a 1.5 molar ratio of ligand to protein, ca. 10 mg/mL, was prepared. 4.0 ul of this solution was mixed with 3.0 ul of a precipitant solution containing 0.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES, and 20% v/v 2-propanol (Hampton crystal screen I, condition no. 27), and allowed to equilibrate with 350 ul of the aforementioned precipitant well solution. Usable crystals grew after 4 weeks
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.225 α = 90 b = 62.72 β = 90 c = 90.137 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++ 2011-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 1.78 51.48 94.6 0.072 14.1 5.6 17182
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 1.78 1.84 79.9 0.544 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (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 4P9V 2 51.48 11844 645 96.55 0.2039 0.2001 0.2006 0.2754 0.2754 RANDOM 29.501
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] 2.65 -1.47 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.213 r_dihedral_angle_3_deg 18.638 r_dihedral_angle_4_deg 15.948 r_dihedral_angle_1_deg 7.868 r_angle_refined_deg 1.887 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1668 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 96
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing