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Crystal structure of the cAMP-dependent protein kinase A in complex with 1,7-Naphthyridin-8-amine (soaked) and PKI (5-24)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 277 0.2 mM PKA, 100 mM MBT (MES/Bis-Tris Puffer pH 6.9), 1 mM DTT, 0.1 mM EDTA, 75 mM LiCl, 0.2 mM Mega8, 0.5 mM PKI and 18-23% (v/v) Methanol. Soaking in buffer described above with 10% (v/v) 1,7-Naphthydrin-8-amine in DMSO (1M stock) and 30% (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 2.63 53.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.406 α = 90 b = 74.264 β = 90 c = 80.225 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 2019-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918400 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.898 43.542 99.2 0.056 18.8 4.4 34597 24.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2.01 98.4 0.496 3.02
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6F14 1.9 43.54 1.35 34586 1730 99.14 0.1892 0.1875 0.188 0.2207 0.2215 26.92
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 20.4374 f_angle_d 0.7271 f_chiral_restr 0.0497 f_bond_d 0.0059 f_plane_restr 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2848 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 23
Software Software Software Name Purpose PHASER phasing PHENIX refinement XDS data reduction XDS data scaling Coot model building