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Crystal structure of the Grb2 SH2 domain in complex with a tripeptide: Ac-pY-Ac6c-N-phenylpropyl
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, 10 mg/mL, was prepared. 4.0 ul of this solution was mixed with 3.0 ul precipitant solution containing 0.1 M HEPES, pH 7.5, and 25% w/v polyethylene glycol, MW 10,000, and allowed to equilibrate with 350 ul of the aforementioned precipitant well solution at 298 K. Useable crystals grew after 4 weeks
Crystal Properties Matthews coefficient Solvent content 2.11 41.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.01 α = 90 b = 62.977 β = 90 c = 90.889 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++ 2011-05-18 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 1.8 51.76 84.6 0.04 46.7 10.2 16789
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 1.8 1.86 92.4 0.113 10.5
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 1.8 51.76 15867 850 84.44 0.1802 0.1769 0.1759 0.2448 0.2446 RANDOM 23.136
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] 2.9 -2.4 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.585 r_dihedral_angle_3_deg 15.747 r_dihedral_angle_4_deg 13.322 r_dihedral_angle_1_deg 6.14 r_angle_refined_deg 2.019 r_chiral_restr 0.164 r_bond_refined_d 0.023 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1652 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 106
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction