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Crystal structure of the cAMP-dependent protein kinase A with a chiral ligand (S- and E-configuration, soaked)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SPY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 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 44.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.781 α = 90 b = 71.775 β = 90 c = 97.325 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 PILATUS3 2M 2020-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.82656 BESSY 14.2
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 1.37 45.71 99.5 0.034 21.23 4.4 76558 15.66
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 1.37 1.45 99.1 0.468 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 6SPY 1.37 25.22 1.36 76543 3825 99.46 0.1534 0.152 0.1553 0.1789 0.1833 20.35
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 22.862 f_angle_d 0.9376 f_chiral_restr 0.0779 f_bond_d 0.0074 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2712 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XDS data scaling PHASER phasing