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Crystal structure of the catalytic subunit of cAMP-dependent protein kinase displaying partial phosphoryl transfer of AMP-PNP onto a substrate peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277.15 50 mM Bicine, 150 mM Ammonium acetate, 10 mM DTT, ~7-10 mg/mL protein
Well solution: 2% MPD in a 1 mL well. 80 uL of methanol was added to the well immediately before sealing.
Drop was 8 uL of 1:1 protein:well, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.63 53.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.69 α = 90 b = 79.8 β = 90 c = 98.14 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 CCD ADSC QUANTUM 315r
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.55 61.91 99.7 0.076 12.8 5.7 66294
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.63 99.2 0.446 3.2 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.55 61.91 62785 3357 99.51 0.17292 0.17176 0.171 0.19448 0.1932 RANDOM 15.146
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] 0.57 -0.53 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.373 r_dihedral_angle_4_deg 17.404 r_dihedral_angle_3_deg 13.293 r_dihedral_angle_1_deg 5.394 r_scangle_it 3.011 r_scbond_it 1.86 r_angle_refined_deg 1.329 r_mcangle_it 1.253 r_mcbond_it 0.666 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.373 r_dihedral_angle_4_deg 17.404 r_dihedral_angle_3_deg 13.293 r_dihedral_angle_1_deg 5.394 r_scangle_it 3.011 r_scbond_it 1.86 r_angle_refined_deg 1.329 r_mcangle_it 1.253 r_mcbond_it 0.666 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2936 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling