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Structure of cAMP-dependent protein kinase using a MD-MX procedure, produced using 2.4 Angstrom data
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FJQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 20% PEG 4000, 0.05 M MES pH 5.2, 0.05 M MgCl2, and 0.005 M DTT
Crystal Properties Matthews coefficient Solvent content 2.72 54.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.976 α = 90 b = 79.744 β = 90 c = 99.058 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 285 PIXEL DECTRIS PILATUS3 S 6M Primary Mirror: Flat; Secondary Mirror: uncooled cyllindrical silicon bent into torroid; 2:1 demagnification; Both mirrors coated with Pt/Rh 2018-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11583 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.4 49.53 99.94 0.1829 0.1905 0.05272 0.993 15.9 13 18876 21.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.486 100 0.7015 0.7294 0.1974 0.959 13.7
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 3FJQ 2.4 49.53 1.34 18874 1888 99.94 0.1331 0.1282 0.1279 0.1765 0.1758 29.76
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 20.5542 f_angle_d 0.7785 f_chiral_restr 0.0439 f_plane_restr 0.0076 f_bond_d 0.0037
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2929 Nucleic Acid Atoms Solvent Atoms 496 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement PHASER phasing DIALS data reduction xia2 data reduction Aimless data scaling BLEND data scaling