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Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-2-aminodeoxymannojirimycin
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 7.4 292 3M sodium acetate, pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.45 49.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.101 α = 90 b = 108.101 β = 90 c = 67.507 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 2017-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 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 1.13 76.44 99.1 0.069 0.075 0.026 0.999 10.2 7.5 143559 13.59
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 1.13 1.15 86 1.501 1.682 0.735 0.4 1 4.8
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 1.13 76.44 136411 7133 99.02 0.12332 0.12222 0.1216 0.14411 0.1429 RANDOM 17.888
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] -0.31 -0.31 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.362 r_sphericity_free 28.34 r_dihedral_angle_4_deg 18.072 r_dihedral_angle_3_deg 12.507 r_sphericity_bonded 8.362 r_dihedral_angle_1_deg 5.918 r_long_range_B_refined 3.128 r_long_range_B_other 2.64 r_scangle_other 1.995 r_mcangle_other 1.646
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.362 r_sphericity_free 28.34 r_dihedral_angle_4_deg 18.072 r_dihedral_angle_3_deg 12.507 r_sphericity_bonded 8.362 r_dihedral_angle_1_deg 5.918 r_long_range_B_refined 3.128 r_long_range_B_other 2.64 r_scangle_other 1.995 r_mcangle_other 1.646 r_mcangle_it 1.642 r_scbond_it 1.611 r_scbond_other 1.61 r_angle_refined_deg 1.495 r_rigid_bond_restr 1.483 r_mcbond_it 1.276 r_mcbond_other 1.269 r_angle_other_deg 1.026 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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 2829 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing