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beta2 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclodextrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F15
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 281.15 in 0.2 M lithium chloride, 20% w/v PEG 6000 and 0.1 M sodium HEPES pH 7
Crystal Properties Matthews coefficient Solvent content 2.64 53.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.538 α = 90 b = 96.432 β = 125.46 c = 118.724 γ = 90
Symmetry Space Group C 1 2 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 210r 2013-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.953700 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2 48.38 99.9 0.084 0.098 16.9 7.6 127116
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 2.03 97.8 0.668 2.8 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2F15 2 43.38 120729 6385 99.87 0.1715 0.16872 0.1774 0.22463 0.2305 RANDOM 32.5
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] -0.35 0.2 0.51 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.336 r_dihedral_angle_4_deg 21.549 r_dihedral_angle_3_deg 11.503 r_long_range_B_refined 7.494 r_long_range_B_other 7.493 r_dihedral_angle_1_deg 6.882 r_scangle_other 3.017 r_mcangle_it 2.096 r_mcangle_other 2.096 r_scbond_it 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.336 r_dihedral_angle_4_deg 21.549 r_dihedral_angle_3_deg 11.503 r_long_range_B_refined 7.494 r_long_range_B_other 7.493 r_dihedral_angle_1_deg 6.882 r_scangle_other 3.017 r_mcangle_it 2.096 r_mcangle_other 2.096 r_scbond_it 1.97 r_scbond_other 1.97 r_angle_refined_deg 1.68 r_mcbond_it 1.281 r_mcbond_other 1.281 r_angle_other_deg 0.785 r_chiral_restr 0.113 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11966 Nucleic Acid Atoms Solvent Atoms 1677 Heterogen Atoms 1698
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing Aimless data scaling XDS data reduction Blu-Ice data collection