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Crystal structure of human AMPK alpha1 KD-AID with K43A mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H6D PDB ENTRY 2H6D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.5 M HNa2PO4/0.5 M HK2PO4, 0.1 M Tris hydrochloride, pH 8.5, 0.1 M H(NH4)2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.532 α = 90 b = 119.532 β = 90 c = 215.639 γ = 90
Symmetry Space Group I 41 2 2
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 MARMOSAIC 300 mm CCD 2012-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07806 APS 21-ID-D
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 2.95 30 100 0.096 32.3 17.3 16876 16876
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.06 100
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 PDB ENTRY 2H6D 2.95 29.9 15669 15630 1222 99.75 0.23312 0.2297 0.2277 0.27681 0.2745 RANDOM 72.763
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] -2.01 -2.01 4.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.604 r_dihedral_angle_4_deg 20.084 r_dihedral_angle_3_deg 16.654 r_long_range_B_refined 12.426 r_long_range_B_other 12.425 r_scangle_other 7.386 r_mcangle_it 7.384 r_mcangle_other 7.383 r_dihedral_angle_1_deg 5.799 r_scbond_it 4.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.604 r_dihedral_angle_4_deg 20.084 r_dihedral_angle_3_deg 16.654 r_long_range_B_refined 12.426 r_long_range_B_other 12.425 r_scangle_other 7.386 r_mcangle_it 7.384 r_mcangle_other 7.383 r_dihedral_angle_1_deg 5.799 r_scbond_it 4.863 r_scbond_other 4.856 r_mcbond_it 4.787 r_mcbond_other 4.787 r_angle_refined_deg 1.445 r_angle_other_deg 0.89 r_chiral_restr 0.069 r_bond_other_d 0.011 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5293 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling