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Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-glucosamine)
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 7 292 3 M sodium acetate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.28 46.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.772 α = 90 b = 108.772 β = 90 c = 67.703 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 2015-08-06 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) 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 1.27 39.5 100 0.058 0.063 0.024 0.999 13.1 6.6 103773 14
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 1.27 1.29 100 1.295 1.409 0.55 0.515 1.4 6.4
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 5M17 1.27 39.5 98601 5172 99.93 0.13342 0.13232 0.1299 0.15413 0.1532 RANDOM 18.208
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] -0.84 -0.84 1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.822 r_sphericity_free 23.555 r_dihedral_angle_4_deg 16.892 r_sphericity_bonded 13.646 r_dihedral_angle_3_deg 12.339 r_dihedral_angle_1_deg 8.845 r_long_range_B_refined 2.792 r_long_range_B_other 2.631 r_scangle_other 2.241 r_scbond_it 1.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.822 r_sphericity_free 23.555 r_dihedral_angle_4_deg 16.892 r_sphericity_bonded 13.646 r_dihedral_angle_3_deg 12.339 r_dihedral_angle_1_deg 8.845 r_long_range_B_refined 2.792 r_long_range_B_other 2.631 r_scangle_other 2.241 r_scbond_it 1.959 r_scbond_other 1.956 r_mcangle_it 1.826 r_mcangle_other 1.826 r_rigid_bond_restr 1.774 r_angle_refined_deg 1.585 r_angle_other_deg 1.515 r_mcbond_it 1.435 r_mcbond_other 1.434 r_chiral_restr 0.092 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 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 2809 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing