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Beta-L-Arabinofurano-cyclitol Aziridines are Cysteine-directed Broad-spectrum Inhibitors and Activity-based Probes for Retaining Beta-L-arabinofuranosidases
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.7 M sodium citrate, 0.1 M MES pH 6.5, 10 mM dithiothreitol
Crystal Properties Matthews coefficient Solvent content 2.95 58.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.26 α = 90 b = 77.26 β = 90 c = 254.647 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS EIGER2 XE 16M 2022-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 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 2.35 85.03 100 0.199 0.995 7.7 20 37850
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 100 0.938 0.66 0.7
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 2.35 85.03 35892 1886 100 0.20933 0.20685 0.2103 0.25426 0.257 RANDOM 69.408
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] 1.63 0.82 1.63 -5.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.215 r_dihedral_angle_2_deg 10.304 r_long_range_B_refined 9.968 r_long_range_B_other 9.968 r_scangle_other 8.38 r_mcangle_other 8.271 r_mcangle_it 8.266 r_dihedral_angle_1_deg 6.9 r_mcbond_it 6.147 r_mcbond_other 6.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.215 r_dihedral_angle_2_deg 10.304 r_long_range_B_refined 9.968 r_long_range_B_other 9.968 r_scangle_other 8.38 r_mcangle_other 8.271 r_mcangle_it 8.266 r_dihedral_angle_1_deg 6.9 r_mcbond_it 6.147 r_mcbond_other 6.144 r_scbond_it 6.088 r_scbond_other 6.087 r_angle_refined_deg 1.407 r_angle_other_deg 0.471 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 5096 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing