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cAMP-dependent Protein Kinase A from cricetulus griseus in complex with fragment like molecule 4-{3-[(1H-1,2,4-Triazol-1-yl)methyl]phenyl}-1H-pyrrolo[2,3-b]pyridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N1F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 277 30 mM MES-BIS-TRIS pH 6.9, 0.03 mM Mega8-Solution, 1 mM DTT, 0.1 mM EDTA, 75 mM LiCl, 0.07 mM PKI (Sigma: P7739) 24% Methanol in reservoir
30% MPD for cryoprotection
Crystal Properties Matthews coefficient Solvent content 2.6 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.792 α = 90 b = 71.408 β = 90 c = 97.578 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 EIGER X 16M KB-mirrors 2025-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976250 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 1.38 48.79 99.9 0.082 0.085 0.999 16 13.1 75034 16.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.38 1.46 99.6 0.818 0.856 0.848 2 11.5
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 1.38 29.4 1.37 75007 3750 99.88 0.146 0.1446 0.1448 0.1714 0.1717 20.21
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 13.039 f_angle_d 0.9372 f_chiral_restr 0.078 f_plane_restr 0.0097 f_bond_d 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2748 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XDS data scaling PHASER phasing