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Crystal structure of Amylase 5 (Amy5) from Ruminococcus bromii 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 7JJT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 0.1 M SPG pH 9.0, 25% w/v PEG 1500, 1 mM 4'-octylamine-a-D-maltotriose epicyclophellitol (compound 2a)
Crystal Properties Matthews coefficient Solvent content 2.05 40.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.869 α = 90 b = 94.873 β = 94.64 c = 49.904 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 PIXEL DECTRIS EIGER2 XE 16M 2023-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.7446 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 1.4 44.05 99.4 0.16 1 6.9 7 90248
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 1.4 1.42 0.41
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 1.4 44.05 85535 4612 99.25 0.18915 0.18739 0.1963 0.22234 0.2306 RANDOM 14.298
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] -0.22 -0.46 0.39 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.255 r_dihedral_angle_2_deg 7.437 r_dihedral_angle_1_deg 6.661 r_long_range_B_refined 4.003 r_long_range_B_other 3.818 r_scangle_other 2.56 r_scbond_it 1.747 r_scbond_other 1.747 r_angle_refined_deg 1.69 r_mcangle_other 1.534
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.255 r_dihedral_angle_2_deg 7.437 r_dihedral_angle_1_deg 6.661 r_long_range_B_refined 4.003 r_long_range_B_other 3.818 r_scangle_other 2.56 r_scbond_it 1.747 r_scbond_other 1.747 r_angle_refined_deg 1.69 r_mcangle_other 1.534 r_mcangle_it 1.533 r_mcbond_it 1.074 r_mcbond_other 1.065 r_angle_other_deg 0.632 r_chiral_restr 0.269 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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 4027 Nucleic Acid Atoms Solvent Atoms 591 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing