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Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C7I PDB entry 3C7I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS,30% w/v polyethylene glycol 4,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.82 30.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.935 α = 90 b = 41.935 β = 90 c = 108.971 γ = 90
Symmetry Space Group P 43 21 2
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++ 2010-07-27 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 Sym 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 1.82 50 93.7 0.076 22.5 11.8 8801
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.89 96.4 0.223 10.1 12.6 900
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 PDB entry 3C7I 1.82 26.05 8310 411 93.74 0.1812 0.17746 0.1746 0.2597 0.2539 RANDOM 21.029
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] -0.07 -0.07 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.598 r_dihedral_angle_4_deg 17.742 r_dihedral_angle_3_deg 14.186 r_dihedral_angle_1_deg 7.481 r_scangle_it 4.233 r_scbond_it 2.986 r_angle_refined_deg 2.033 r_mcangle_it 2.022 r_mcbond_it 1.312 r_chiral_restr 0.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.598 r_dihedral_angle_4_deg 17.742 r_dihedral_angle_3_deg 14.186 r_dihedral_angle_1_deg 7.481 r_scangle_it 4.233 r_scbond_it 2.986 r_angle_refined_deg 2.033 r_mcangle_it 2.022 r_mcbond_it 1.312 r_chiral_restr 0.142 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 872 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling