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Crystal structure of the cAMP-dependent protein kinase A in complex with phenol
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
Soaking: 100mM phenol in buffer described above and 30% MPD
Crystal Properties Matthews coefficient Solvent content 2.19 43.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.775 α = 90 b = 71.385 β = 90 c = 97.41 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 2019-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91840 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 1.379 48.705 99.8 0.042 21.7 6.5 74984 15.85
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 1.38 1.46 0.497 3.07
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 1.38 20.12 1.37 74955 3748 99.8 0.1465 0.1451 0.1464 0.1736 0.1729 20.12
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 22.5984 f_angle_d 0.9353 f_chiral_restr 0.0774 f_bond_d 0.0067 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2714 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 27
Software Software Software Name Purpose Coot model building PHENIX refinement XDS data reduction XDS data scaling PHASER phasing