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Structure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex alpha-Glc-1,3-(1,2-anhydro-carba-mannose)
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 45.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.233 α = 90 b = 108.233 β = 90 c = 67.446 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 1.12 76.53 100 0.063 0.069 0.027 0.999 9.8 6.4 149038 12.79
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 1.12 1.14 99.2 1.387 1.528 0.834 0.45 1.1 5.7
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 5M17 1.12 76.53 141622 7398 99.91 0.12657 0.12555 0.1252 0.14589 0.1459 RANDOM 17.07
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] -0.05 -0.05 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.335 r_sphericity_free 26.908 r_dihedral_angle_4_deg 19.833 r_dihedral_angle_3_deg 12.252 r_dihedral_angle_1_deg 8.981 r_sphericity_bonded 7.475 r_long_range_B_refined 2.927 r_long_range_B_other 2.547 r_scangle_other 1.952 r_rigid_bond_restr 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.335 r_sphericity_free 26.908 r_dihedral_angle_4_deg 19.833 r_dihedral_angle_3_deg 12.252 r_dihedral_angle_1_deg 8.981 r_sphericity_bonded 7.475 r_long_range_B_refined 2.927 r_long_range_B_other 2.547 r_scangle_other 1.952 r_rigid_bond_restr 1.76 r_scbond_it 1.623 r_scbond_other 1.622 r_mcangle_other 1.575 r_mcangle_it 1.572 r_angle_refined_deg 1.557 r_mcbond_it 1.211 r_mcbond_other 1.206 r_angle_other_deg 1.09 r_chiral_restr 0.101 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 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 2818 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing