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Crystal structures of the kinase domain of PKA in complex with ATP-competitive inhibitors
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 273 13-17% PEG 3K-20K, 100 mM MES pH 6.5 or acetate 4.6, 1-15% methanol. Seeded, pH 4.5 - 6.5, vapor diffusion, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.7 54.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.46 α = 90 b = 96.392 β = 102.66 c = 180.036 γ = 90
Symmetry Space Group P 1 21 1
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 210 un-focused beam 2005-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
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 2.2 50 98.2 0.079 4.3 137412 2
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 2.2 2.28 97.3 0.6 4.2
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 THROUGHOUT 2.2 46.93 127573 6773 95.82 0.26499 0.26365 0.2625 0.28988 0.2856 RANDOM 14.349
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] -1.65 -1.98 -0.35 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.604 r_dihedral_angle_4_deg 18.049 r_dihedral_angle_3_deg 15.535 r_dihedral_angle_1_deg 5.044 r_angle_refined_deg 1.195 r_angle_other_deg 0.928 r_scangle_it 0.788 r_scbond_it 0.519 r_mcangle_it 0.405 r_mcbond_it 0.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.604 r_dihedral_angle_4_deg 18.049 r_dihedral_angle_3_deg 15.535 r_dihedral_angle_1_deg 5.044 r_angle_refined_deg 1.195 r_angle_other_deg 0.928 r_scangle_it 0.788 r_scbond_it 0.519 r_mcangle_it 0.405 r_mcbond_it 0.253 r_symmetry_vdw_other 0.238 r_nbd_other 0.178 r_nbd_refined 0.176 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.156 r_mcbond_other 0.119 r_chiral_restr 0.085 r_nbtor_other 0.079 r_xyhbond_nbd_other 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17921 Nucleic Acid Atoms Solvent Atoms 762 Heterogen Atoms 204
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction JDirector data collection HKL-2000 data reduction AMoRE phasing