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Crystal structure of the protein kinase domain of yeast AMP-activated protein kinase Snf1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 294 100 mM Tris (pH 8.5), 25% (w/v) PEG3350, and 300 mM (NH4)2SO4, VAPOR DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.42 49.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.028 α = 90 b = 75.137 β = 90 c = 113.699 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 4 2005-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A NSLS X4A
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 30 99 0.062 4.2 42125 31518 3 3
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 2.256 99 0.605 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 2.2 19.73 29855 29853 1570 99.7 0.24114 0.23913 0.237 0.28 0.2752 RANDOM 45.678
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] 0.29 -0.2 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.326 r_dihedral_angle_4_deg 20.439 r_dihedral_angle_3_deg 16.53 r_dihedral_angle_1_deg 5.374 r_scangle_it 2.377 r_scbond_it 1.562 r_angle_refined_deg 1.229 r_mcangle_it 1.073 r_mcbond_it 0.833 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.326 r_dihedral_angle_4_deg 20.439 r_dihedral_angle_3_deg 16.53 r_dihedral_angle_1_deg 5.374 r_scangle_it 2.377 r_scbond_it 1.562 r_angle_refined_deg 1.229 r_mcangle_it 1.073 r_mcbond_it 0.833 r_nbtor_refined 0.302 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.177 r_symmetry_vdw_refined 0.132 r_symmetry_hbond_refined 0.113 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3851 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling