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Protein Kinase Domain of the Human 5'-AMP-activated protein kinase catalytic subunit alpha-2 (AMPK alpha-2 chain)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FH9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 18.6% PEG 4000, 0.1M AmSO4, 0.1M Tris-HCl pH 8.5, 15%v/v isopropanol,5mM ATP/MgCl, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.13 42.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.454 α = 90 b = 67.41 β = 91.3 c = 50.493 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 IMAGE PLATE RIGAKU RAXIS IV 2006-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.85 19.72 98.8 0.047 26.91 3.5 22387 22387 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.88 83 0.504 1.6 2.3 930
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 2FH9 1.85 19.72 22636 21209 1147 98.76 0.19003 0.18803 0.1872 0.22674 0.2255 RANDOM 28.52
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] -0.7 -0.57 0.64 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.287 r_dihedral_angle_4_deg 16.364 r_dihedral_angle_3_deg 16.266 r_dihedral_angle_1_deg 5.501 r_scangle_it 5.356 r_scbond_it 3.926 r_mcangle_it 2.728 r_mcbond_it 1.997 r_angle_refined_deg 1.513 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.287 r_dihedral_angle_4_deg 16.364 r_dihedral_angle_3_deg 16.266 r_dihedral_angle_1_deg 5.501 r_scangle_it 5.356 r_scbond_it 3.926 r_mcangle_it 2.728 r_mcbond_it 1.997 r_angle_refined_deg 1.513 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.12 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2068 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms
Software Software Software Name Purpose SBC-Collect data collection HKL-2000 data reduction PHASER phasing RESOLVE model building ARP/wARP model building REFMAC refinement HKL-2000 data scaling RESOLVE phasing