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GH146 beta-L-arabinofuranosidase bound to covalent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OPJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 10 mg/mL enzyme treated with 200 uM inhibitor at 37C for 16 hours and subsequently mixed 1:1 with 20% PEG3350, 0.2 M ammonium formate, 170 mM arabinose, 0.1 M pH 6.0 MES
Crystal Properties Matthews coefficient Solvent content 2.35 47.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.418 α = 90 b = 95.418 β = 90 c = 189.068 γ = 90
Symmetry Space Group P 43 21 2
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 X 16M 2019-09-14 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) Rrim I (All) 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 1.41 95.42 100 0.12 1 11.7 16.2 167826
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.41 1.43 98.1 3.073 0.5 1.1 16.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5OPJ 1.41 85.33 167656 8404 96.983 0.131 0.1286 0.1285 0.17 0.1699 20.174
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] -0.057 -0.057 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.863 r_dihedral_angle_4_deg 20.822 r_dihedral_angle_other_3_deg 18.239 r_dihedral_angle_3_deg 11.82 r_dihedral_angle_1_deg 6.862 r_scangle_other 3.996 r_scangle_it 3.994 r_rigid_bond_restr 3.925 r_lrange_it 3.787 r_lrange_other 3.734
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.863 r_dihedral_angle_4_deg 20.822 r_dihedral_angle_other_3_deg 18.239 r_dihedral_angle_3_deg 11.82 r_dihedral_angle_1_deg 6.862 r_scangle_other 3.996 r_scangle_it 3.994 r_rigid_bond_restr 3.925 r_lrange_it 3.787 r_lrange_other 3.734 r_scbond_it 3.557 r_scbond_other 3.405 r_mcangle_it 2.964 r_mcangle_other 2.964 r_mcbond_it 2.614 r_mcbond_other 2.614 r_angle_refined_deg 1.877 r_angle_other_deg 1.604 r_symmetry_nbd_refined 0.333 r_nbd_other 0.253 r_nbd_refined 0.228 r_symmetry_xyhbond_nbd_refined 0.196 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.112 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.038 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6099 Nucleic Acid Atoms Solvent Atoms 573 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing