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Crystal structure of the cAMP-dependent protein kinase A in complex with Pyrido[3,2-d]pyrimidin-4-amine (soaked)
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, SITTING DROP 6.9 277 0,2 mM PKA in 100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 mM Mega 8 and 23 % methanol (v/v) 0.003 mL drop volume, 0.5 mL reservoir volume
Crystal Properties Matthews coefficient Solvent content 2.2 44.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.895 α = 90 b = 71.446 β = 90 c = 97.445 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 2018-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91840 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 1.73 45.805 98.1 0.063 14.92 4.4 37845 19.69
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 1.73 1.83 97.6 0.49 2.74
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 1.73 45.8 1.36 37823 1892 98.08 0.181 0.1791 0.1801 0.2164 0.2165 22.94
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 15.4291 f_angle_d 0.7677 f_chiral_restr 0.0521 f_bond_d 0.0061 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2710 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 11
Software Software Software Name Purpose PHASER phasing PHENIX refinement XDS data reduction XDS data scaling Coot model building