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Crystal structure of the c-Src-SH3 domain in complex with the high affinity peptide VSL12
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 7.5 298 1.7 M Ammonium sulphate, 0.1 M Hepes, 5 mM NiCl2 and 10% Glycerol, pH 7.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.81 32.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.904 α = 90 b = 41.046 β = 90 c = 44.066 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 PIXEL DECTRIS PILATUS 6M 2013-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979491 ALBA XALOC
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 0.98 41.05 98.1 0.047 12.5 3.1 34999 34334 9.43
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 0.98 1 89.6 0.836 1.4 2.8 1586
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 THROUGHOUT 4JZ4 0.979 30.035 0.01 66409 65154 3256 98.11 0.1435 0.1427 0.1367 0.1584 0.1518 random 14.6664
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 11.098 f_angle_d 1.381 f_chiral_restr 0.083 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 549 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 7
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction autoPROC data scaling PHASER phasing