☰ Navigation Tabs
Structure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with tetramannoside yeast mannan fragment
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 292 3M sodium acetate, pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.24 45.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.873 α = 90 b = 107.873 β = 90 c = 67.626 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 2016-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9796 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 1.07 76.28 100 0.061 0.067 0.026 0.997 10.6 6.3 170023 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 1.07 1.09 99.3 1.531 1.692 0.705 0.398 1 5.5
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 1.07 76.28 161599 8420 99.92 0.12097 0.12007 0.1193 0.13814 0.137 RANDOM 16.738
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] -0.65 -0.65 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.573 r_sphericity_free 28.441 r_dihedral_angle_4_deg 20.011 r_dihedral_angle_3_deg 12.788 r_sphericity_bonded 9.314 r_dihedral_angle_1_deg 5.696 r_long_range_B_refined 2.897 r_long_range_B_other 2.612 r_scangle_other 2.05 r_scbond_it 1.693
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.573 r_sphericity_free 28.441 r_dihedral_angle_4_deg 20.011 r_dihedral_angle_3_deg 12.788 r_sphericity_bonded 9.314 r_dihedral_angle_1_deg 5.696 r_long_range_B_refined 2.897 r_long_range_B_other 2.612 r_scangle_other 2.05 r_scbond_it 1.693 r_scbond_other 1.692 r_rigid_bond_restr 1.689 r_angle_refined_deg 1.539 r_mcangle_other 1.531 r_mcangle_it 1.528 r_mcbond_it 1.119 r_mcbond_other 1.108 r_angle_other_deg 1.022 r_chiral_restr 0.099 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 2789 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing