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Joint X-ray/neutron structure of PKAc with products Sr2-ADP and phosphorylated peptide SP20
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IAY PDB entry 4IAY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 100 mM MES, pH 6.5, 5 mM DTT, PEG4000
Crystal Properties Matthews coefficient Solvent content 2.71 54.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.332 α = 90 b = 79.898 β = 90 c = 100.292 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 293 IMAGE PLATE RIGAKU RAXIS IV++ osmic varimax 2015-09-15 M SINGLE WAVELENGTH 2 1 neutron 293 IMAGE PLATE LADI III collimators 2015-09-18 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54 2 NUCLEAR REACTOR ILL BEAMLINE LADI III 2.8-4.0 ILL LADI III
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 40 91.7 0.069 14.3 4.2 30175 2 2.5 40 62 0.153 7.7 3.4 10426
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 0.542 4.2 2 2.5 2.64 0.181 1.9
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2 40 3 24119 1170 73.3 0.187 0.1967 0.217 0.2012 random 30.03 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.5 40 3 10012 474 60 0.226 0.275 random 30.03
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 x_torsion_deg 29.5 x_torsion_deg 29.5 x_angle_deg 1 x_angle_deg 1 x_torsion_impr_deg 0.71 x_torsion_impr_deg 0.71 x_bond_d 0.008 x_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2940 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 29
Software Software Software Name Purpose nCNS refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing LAUEGEN data reduction LSCALE data scaling CNS phasing