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Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-noeuromycin and 1,2-alpha-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 7.2 292 3 M sodium acetate, pH 7.2
Crystal Properties Matthews coefficient Solvent content 2.24 45.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.033 α = 90 b = 108.033 β = 90 c = 67.45 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 2015-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979 Diamond I04
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 1.05 57.21 99.3 0.054 0.999 10.8 5.9 178974 11.87
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 1.05 1.07 89.1 1.314 0.308 0.7 2.7
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 1.05 57.21 170072 8872 99.3 0.11581 0.11488 0.1146 0.13339 0.1328 RANDOM 16.677
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] 0.25 0.25 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.32 r_sphericity_free 35.197 r_dihedral_angle_4_deg 18.249 r_dihedral_angle_3_deg 12.123 r_sphericity_bonded 10.291 r_dihedral_angle_1_deg 8.712 r_long_range_B_refined 3.72 r_long_range_B_other 3.183 r_rigid_bond_restr 2.387 r_scangle_other 1.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.32 r_sphericity_free 35.197 r_dihedral_angle_4_deg 18.249 r_dihedral_angle_3_deg 12.123 r_sphericity_bonded 10.291 r_dihedral_angle_1_deg 8.712 r_long_range_B_refined 3.72 r_long_range_B_other 3.183 r_rigid_bond_restr 2.387 r_scangle_other 1.985 r_scbond_it 1.75 r_scbond_other 1.75 r_angle_refined_deg 1.673 r_mcangle_it 1.634 r_mcangle_other 1.634 r_mcbond_it 1.236 r_mcbond_other 1.235 r_angle_other_deg 1.157 r_chiral_restr 0.108 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 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 2813 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing