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Crystal structure of the c-Src-SH3 domain in complex with the high affinity peptide APP12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 1.6M Ammonium sulphate, 0.1M sodium acetate and 10% Glycerol, pH 4.0, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.99 38.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.91 α = 90 b = 32.85 β = 104.45 c = 31.64 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315r vertical focusing mirror (VFM) and a horizontal focusing mirror (HFM), manufactured by IRELEC. 2012-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9334 ESRF ID14-4
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 1.28 20.03 99.8 0.049 20.8 4.4 17089 17055 7.19
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 1.28 1.3 96.1 0.181 7.2 3.9 876
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 0.1170 4JZ4 1.279 20.03 0.18 33223 33153 1584 99.79 0.117 0.116 0.117 0.1371 0.1359 random 10.6406
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.088 f_angle_d 1.287 f_chiral_restr 0.07 f_bond_d 0.01 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 569 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 5
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction PHASER phasing