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Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-1,2-dideoxymannose and alpha-1,2-mannobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UTF modified 4UTF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 3 M sodium acetate, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.26 45.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.4 α = 90 b = 108.4 β = 90 c = 67.587 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 2015-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
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 1.04 76.65 99 0.052 0.994 13 6 184688 12.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.04 1.06 87.3 1.063 0.427 1 3.5
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 (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 modified 4UTF 1.04 76.65 175534 9151 98.98 0.11934 0.11863 0.1179 0.13299 0.1323 RANDOM 16.113
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] -0.26 -0.26 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.083 r_sphericity_free 30.272 r_dihedral_angle_4_deg 19.243 r_dihedral_angle_3_deg 12.449 r_dihedral_angle_1_deg 8.189 r_sphericity_bonded 7.644 r_long_range_B_refined 3.122 r_long_range_B_other 2.637 r_scangle_other 1.896 r_rigid_bond_restr 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.083 r_sphericity_free 30.272 r_dihedral_angle_4_deg 19.243 r_dihedral_angle_3_deg 12.449 r_dihedral_angle_1_deg 8.189 r_sphericity_bonded 7.644 r_long_range_B_refined 3.122 r_long_range_B_other 2.637 r_scangle_other 1.896 r_rigid_bond_restr 1.77 r_angle_refined_deg 1.609 r_scbond_it 1.558 r_scbond_other 1.554 r_mcangle_other 1.408 r_mcangle_it 1.404 r_angle_other_deg 1.089 r_mcbond_it 1.025 r_mcbond_other 1.002 r_chiral_restr 0.102 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2822 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing