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Crystal structure of the N114Q mutant of ABL-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O88 PDB entry 2o88
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 288 2M ammonium sulphate, 0.4 M NaCl, 0.1 M sodium citrate, 10% glycerol, pH 3.5, vapor diffusion, hanging drop, temperature 288K
Crystal Properties Matthews coefficient Solvent content 1.89 34.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.996 α = 90 b = 47.636 β = 90 c = 55.662 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 CCD BRUKER SMART 6000 Montel Optics 2005-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.85 47.636 92.8 0.0653 0.0653 7.6 10944 10158 17.692
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.95 72.5 0.2426 0.2649 3.49 1.26 1123
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 2o88 1.85 18 10098 998 92.77 0.192 0.185 0.1954 0.248 0.2529 RANDOM 16.612
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] 0.14 -0.09 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.555 r_dihedral_angle_4_deg 16.349 r_dihedral_angle_3_deg 15.556 r_dihedral_angle_1_deg 6.363 r_scangle_it 3.849 r_scbond_it 2.825 r_angle_refined_deg 2.106 r_mcangle_it 1.934 r_mcbond_it 1.312 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.555 r_dihedral_angle_4_deg 16.349 r_dihedral_angle_3_deg 15.556 r_dihedral_angle_1_deg 6.363 r_scangle_it 3.849 r_scbond_it 2.825 r_angle_refined_deg 2.106 r_mcangle_it 1.934 r_mcbond_it 1.312 r_nbtor_refined 0.323 r_nbd_refined 0.228 r_symmetry_hbond_refined 0.189 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.151 r_gen_planes_refined 0.014 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1045 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 10
Software Software Software Name Purpose SAINT data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data collection SAINT data reduction SCALA data scaling