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Crystal structure of the N114A mutant of ABL-SH3 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ABQ PDB entry 1ABQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3 288 2M ammonium sulphate, 5% PEG300, 10% glycerol, and 0.1 M of buffer solution, vapor diffusion, hanging drop, temperature 288K
Crystal Properties Matthews coefficient Solvent content 1.76 30.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.819 α = 90 b = 53.096 β = 90 c = 41.296 γ = 90
Symmetry Space Group C 2 2 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 CCD BRUKER SMART 6000 Montel Optics 2006-01-19 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 1.35 41.31 92.3 0.0328 0.0328 6.79 11162 10303 12.829
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 1.35 1.45 82.2 0.1326 0.1326 7.3 3 1734
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 1ABQ 1.4 13.77 9380 442 93.68 0.21 0.208 0.2142 0.24 0.2581 RANDOM 15.844
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] -0.02 0.07 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.061 r_dihedral_angle_3_deg 11.185 r_dihedral_angle_4_deg 11.097 r_dihedral_angle_1_deg 7.659 r_scangle_it 3.78 r_scbond_it 3.335 r_mcangle_it 2.174 r_angle_refined_deg 2.097 r_mcbond_it 1.432 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.061 r_dihedral_angle_3_deg 11.185 r_dihedral_angle_4_deg 11.097 r_dihedral_angle_1_deg 7.659 r_scangle_it 3.78 r_scbond_it 3.335 r_mcangle_it 2.174 r_angle_refined_deg 2.097 r_mcbond_it 1.432 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.273 r_xyhbond_nbd_refined 0.241 r_nbd_refined 0.236 r_symmetry_hbond_refined 0.228 r_chiral_restr 0.12 r_bond_refined_d 0.014 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 491 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 6
Software Software Software Name Purpose SAINT data scaling SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data collection SAINT data reduction