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A carbohydrate esterase family 15 (CE15) glucuronoyl esterase from Phocaeicola ATCC 8482 bound to novel ligand.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QCL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M MES pH 6.0, 20 mM NaCl, and 20-24% (w/v) PEG 6000, soaked in 0.25 M neutralised galacturonic acid.
Crystal Properties Matthews coefficient Solvent content 1.92 35.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.215 α = 90 b = 59.163 β = 101.44 c = 87.163 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 EIGER X 16M 2022-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9762 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.16 85.43 93 0.986 6.7 6.8 28249
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 2.16 2.35 0.476
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 2.16 85.43 26881 1367 70.64 0.18236 0.17884 0.1847 0.25151 0.2539 RANDOM 32.823
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] -0.13 0.2 -0.14 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.735 r_dihedral_angle_4_deg 19.777 r_dihedral_angle_3_deg 17.195 r_dihedral_angle_1_deg 7.657 r_long_range_B_refined 6.21 r_long_range_B_other 6.21 r_scangle_other 4.417 r_mcangle_it 3.615 r_mcangle_other 3.615 r_scbond_it 2.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.735 r_dihedral_angle_4_deg 19.777 r_dihedral_angle_3_deg 17.195 r_dihedral_angle_1_deg 7.657 r_long_range_B_refined 6.21 r_long_range_B_other 6.21 r_scangle_other 4.417 r_mcangle_it 3.615 r_mcangle_other 3.615 r_scbond_it 2.741 r_scbond_other 2.741 r_mcbond_it 2.333 r_mcbond_other 2.333 r_angle_refined_deg 1.483 r_angle_other_deg 1.246 r_chiral_restr 0.068 r_bond_refined_d 0.008 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 6226 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing