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Structure of an E336Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-1,2-anhydro-mannose hydrolyzed by enzyme
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 2.22 44.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.619 α = 90 b = 107.619 β = 90 c = 67.485 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 0.9795 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 1.34 76.1 99.9 0.069 0.075 0.029 0.999 10.6 6.5 86260 15.82
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 1.34 1.36 99.5 1.278 1.392 0.544 0.563 1.3 6.3
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 1.34 76.1 81834 4416 99.92 0.1276 0.12584 0.1255 0.16114 0.1611 RANDOM 20.366
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] -0.15 -0.15 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.373 r_sphericity_free 26.306 r_dihedral_angle_4_deg 17.719 r_dihedral_angle_3_deg 12.455 r_sphericity_bonded 8.636 r_dihedral_angle_1_deg 5.883 r_long_range_B_refined 3.207 r_long_range_B_other 3.022 r_scangle_other 2.444 r_scbond_it 2.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.373 r_sphericity_free 26.306 r_dihedral_angle_4_deg 17.719 r_dihedral_angle_3_deg 12.455 r_sphericity_bonded 8.636 r_dihedral_angle_1_deg 5.883 r_long_range_B_refined 3.207 r_long_range_B_other 3.022 r_scangle_other 2.444 r_scbond_it 2.019 r_scbond_other 2.019 r_mcangle_other 1.955 r_mcangle_it 1.953 r_rigid_bond_restr 1.687 r_mcbond_it 1.559 r_mcbond_other 1.548 r_angle_refined_deg 1.493 r_angle_other_deg 1.043 r_chiral_restr 0.098 r_bond_refined_d 0.011 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 2752 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing