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Crystal structure of integrin-linked kinase (ILK) in complex with alpha-parvin and a cyano-quinoline ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KMU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 277 0.1 M HEPES pH 7.5, 10% w/v Polyethylene glycol 8,000, 8% v/v Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.71 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.86 α = 90 b = 118.37 β = 100.91 c = 47.6 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M-F 2024-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976269 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.5 43.07 98.2 0.03332 0.03332 0.01341 0.999 26.87 7.1 74633 19.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.554 97.29 0.2733 0.294 0.1079 0.965 6.23 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 43.07 1.39 74630 7392 98.2 0.1915 0.189 0.1891 0.215 0.2151 30.54
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 7.7189 f_angle_d 1.1311 f_chiral_restr 0.0616 f_plane_restr 0.0118 f_bond_d 0.0102
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3127 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 63
Software Software Software Name Purpose PHENIX refinement PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing