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Crystal structure of the N114A 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 1BBZ PDB ENTRY 1BBZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Capillary counter diffusion 7 293 Ammoniun sulphate, pH 7, Capillary counter diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 46.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.17 α = 90 b = 50.093 β = 90 c = 56.431 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 Bruker Microstar micro-focus (Montel Optics) 2006-02-02 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 1.75 50 92.2 0.0682 0.0415 16.43 5.9 13236 13236 19.272
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 1.75 1.85 75.8 0.2453 0.219 4.41 2.79 1638
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-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 1BBZ 1.75 20 12531 13178 647 92.18 0.171 0.169 0.1736 0.213 0.2181 RANDOM 24.29
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] -0.17 -0.01 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.415 r_dihedral_angle_4_deg 24.692 r_dihedral_angle_3_deg 14.989 r_dihedral_angle_1_deg 5.543 r_scangle_it 3.443 r_scbond_it 2.361 r_angle_refined_deg 1.744 r_mcangle_it 1.58 r_mcbond_it 1.067 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.415 r_dihedral_angle_4_deg 24.692 r_dihedral_angle_3_deg 14.989 r_dihedral_angle_1_deg 5.543 r_scangle_it 3.443 r_scbond_it 2.361 r_angle_refined_deg 1.744 r_mcangle_it 1.58 r_mcbond_it 1.067 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.301 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.193 r_symmetry_vdw_refined 0.155 r_chiral_restr 0.112 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1037 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data collection SAINT data reduction