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Crystal structure of K38 amylase from Bacillus sp. strain KSM-K38 covalently bound to alpha-1,6 branched pseudo-trisaccharide activity-based probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UD2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5, 34% (w/v) PEG 4000 and 1 mM 4'-octylamine-alpha-D-maltotriose epicyclophellitol (compound 2a).
Crystal Properties Matthews coefficient Solvent content 3.37 63.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.486 α = 90 b = 132.486 β = 90 c = 132.486 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2023-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.02 66.24 100 0.15 1 17.2 41.1 51019
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.07 0.55
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.02 66.24 48345 2598 99.88 0.20336 0.20126 0.2101 0.24173 0.2514 RANDOM 46.529
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.007 r_dihedral_angle_2_deg 7.62 r_dihedral_angle_1_deg 7.334 r_long_range_B_refined 6.928 r_long_range_B_other 6.913 r_scangle_other 5.67 r_mcangle_other 5.15 r_mcangle_it 5.149 r_scbond_it 4.187 r_scbond_other 4.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.007 r_dihedral_angle_2_deg 7.62 r_dihedral_angle_1_deg 7.334 r_long_range_B_refined 6.928 r_long_range_B_other 6.913 r_scangle_other 5.67 r_mcangle_other 5.15 r_mcangle_it 5.149 r_scbond_it 4.187 r_scbond_other 4.187 r_mcbond_it 4.075 r_mcbond_other 4.066 r_angle_refined_deg 1.628 r_angle_other_deg 0.581 r_chiral_restr 0.262 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3890 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing