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Structure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-1,3-mannobiose and alpha-1,2-mannobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M17
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 292 3 M sodium acetate, pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.31 46.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.651 α = 90 b = 108.651 β = 90 c = 68.813 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 PILATUS 6M-F 2016-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.65 76.83 99.6 0.084 0.097 0.047 0.995 8.2 4 47947 25.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 99.8 1.014 1.171 0.578 0.406 1.1 4.1
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5M17 1.65 76.83 45571 2376 99.49 0.14846 0.14633 0.18875 0.1927 RANDOM 26.855
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] 0.81 0.81 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.056 r_sphericity_free 29.337 r_dihedral_angle_4_deg 15.651 r_dihedral_angle_3_deg 12.431 r_sphericity_bonded 10.334 r_dihedral_angle_1_deg 5.71 r_long_range_B_refined 3.962 r_long_range_B_other 3.88 r_scangle_other 3.371 r_mcangle_it 3.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.056 r_sphericity_free 29.337 r_dihedral_angle_4_deg 15.651 r_dihedral_angle_3_deg 12.431 r_sphericity_bonded 10.334 r_dihedral_angle_1_deg 5.71 r_long_range_B_refined 3.962 r_long_range_B_other 3.88 r_scangle_other 3.371 r_mcangle_it 3.027 r_mcangle_other 3.027 r_scbond_it 2.821 r_scbond_other 2.821 r_mcbond_it 2.476 r_mcbond_other 2.475 r_rigid_bond_restr 2.298 r_angle_refined_deg 1.411 r_angle_other_deg 1.008 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2761 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing