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Structure of Inactive E165Q mutant of fungal non-CBM carrying GH26 endo-b-mannanase from Yunnania penicillata in complex with alpha-62-61-di-galactosyl-mannotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZM8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Ammonium sulphate, Hepes pH 7.0.
Crystal Properties Matthews coefficient Solvent content 3.5 64.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.988 α = 90 b = 98.988 β = 90 c = 170.497 γ = 120
Symmetry Space Group P 65 2 2
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 PILATUS3 S 6M 2017-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.92 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.36 34.24 100 20.7 18.2 105928
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.38
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 3zm8 1.36 34.24 100562 5263 99.98 0.12304 0.12197 0.1222 0.14345 0.1434 RANDOM 18.038
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] -0.69 -0.34 -0.69 2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.978 r_sphericity_free 30.616 r_sphericity_bonded 16.852 r_dihedral_angle_4_deg 11.601 r_rigid_bond_restr 10.526 r_dihedral_angle_3_deg 10.01 r_dihedral_angle_1_deg 5.986 r_scbond_other 4.957 r_scbond_it 4.949 r_long_range_B_refined 4.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.978 r_sphericity_free 30.616 r_sphericity_bonded 16.852 r_dihedral_angle_4_deg 11.601 r_rigid_bond_restr 10.526 r_dihedral_angle_3_deg 10.01 r_dihedral_angle_1_deg 5.986 r_scbond_other 4.957 r_scbond_it 4.949 r_long_range_B_refined 4.45 r_long_range_B_other 4.449 r_scangle_other 4.254 r_mcangle_it 2.166 r_mcangle_other 2.166 r_angle_refined_deg 2.095 r_mcbond_it 1.76 r_mcbond_other 1.751 r_angle_other_deg 1.704 r_chiral_restr 0.135 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 2441 Nucleic Acid Atoms Solvent Atoms 485 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing