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Crystal structure of cAMP-dependent protein kinase A (CHO PKA) in complex with 4-Nitrophenol
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 6.9 277 100 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 of 4-Nitrophenol (10% (v/v) in DMSO) in buffer (60% (v/v)) and MPD (30% (v/v)).
Crystal Properties Matthews coefficient Solvent content 2.18 43.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.65 α = 90 b = 71.256 β = 90 c = 97.235 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 1.489 45.614 98 0.038 22.96 4.4 58203 15.92
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 1.49 1.58 0.502 2.85
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 1.49 45.61 1.36 58191 2909 97.93 0.1626 0.1614 0.1624 0.1853 0.187 21.08
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 21.2177 f_angle_d 0.9636 f_chiral_restr 0.0781 f_bond_d 0.0076 f_plane_restr 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2715 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement PHASER phasing XDS data reduction XDS data scaling Coot model building