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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) 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 7.4 292 3 M sodium acetate, pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.25 45.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.175 α = 90 b = 108.175 β = 90 c = 67.575 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 2016-02-19 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) 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 1.03 57.31 98 0.058 0.065 0.028 0.988 12.4 6.1 187832 12.66
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 1.03 1.05 75.8 1.238 1.423 0.679 0.409 1 3.8
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 1.03 57.31 178524 9303 98 0.12484 0.12408 0.1238 0.13935 0.1382 RANDOM 16.585
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] -0.28 -0.28 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.328 r_sphericity_free 24.764 r_dihedral_angle_4_deg 18.352 r_dihedral_angle_3_deg 12.859 r_sphericity_bonded 9.043 r_dihedral_angle_1_deg 5.982 r_long_range_B_refined 3.805 r_long_range_B_other 2.52 r_rigid_bond_restr 2.047 r_scangle_other 1.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.328 r_sphericity_free 24.764 r_dihedral_angle_4_deg 18.352 r_dihedral_angle_3_deg 12.859 r_sphericity_bonded 9.043 r_dihedral_angle_1_deg 5.982 r_long_range_B_refined 3.805 r_long_range_B_other 2.52 r_rigid_bond_restr 2.047 r_scangle_other 1.874 r_angle_refined_deg 1.609 r_scbond_it 1.592 r_scbond_other 1.592 r_mcangle_other 1.458 r_mcangle_it 1.454 r_mcbond_it 1.149 r_mcbond_other 1.138 r_angle_other_deg 1.073 r_chiral_restr 0.108 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 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 2764 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing