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beta1 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclododextrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 281.15 0.2 M lithium sulphate, 25 % w/v PEG 8000 and 0.1 M sodium acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 3.42 58.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.718 α = 111.72 b = 68.394 β = 95.56 c = 92.211 γ = 90.06
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 315r 2013-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953700 Australian Synchrotron MX2
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 1.72 43.71 97.1 0.043 0.06 18.6 3.9 95126
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 1.72 1.75 92.9 0.628 1.9 3.9
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 1Z0M 1.72 43.71 90357 4768 97.08 0.17944 0.17766 0.1856 0.21312 0.2196 RANDOM 25.179
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] -0.54 0.03 -0.3 0.73 -0.07 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.179 r_dihedral_angle_4_deg 15.464 r_dihedral_angle_3_deg 11.75 r_long_range_B_other 7.967 r_long_range_B_refined 7.965 r_dihedral_angle_1_deg 6.076 r_scangle_other 2.091 r_mcangle_it 1.752 r_mcangle_other 1.751 r_angle_refined_deg 1.605
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.179 r_dihedral_angle_4_deg 15.464 r_dihedral_angle_3_deg 11.75 r_long_range_B_other 7.967 r_long_range_B_refined 7.965 r_dihedral_angle_1_deg 6.076 r_scangle_other 2.091 r_mcangle_it 1.752 r_mcangle_other 1.751 r_angle_refined_deg 1.605 r_scbond_it 1.349 r_scbond_other 1.348 r_mcbond_it 1.023 r_mcbond_other 1.023 r_angle_other_deg 0.812 r_chiral_restr 0.105 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 4398 Nucleic Acid Atoms Solvent Atoms 684 Heterogen Atoms 586
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing Aimless data scaling XDS data reduction Blu-Ice data collection