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Crystal structure of GH97 glucodextranase mutant E509Q from Flavobacterium johnsoniae in complex with isomaltotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D73
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 12% PEG20000, 200 mM sodium cacodylate buffer (pH 6.0), 200 mM magnesium acetate, 10 mM glucose
Crystal Properties Matthews coefficient Solvent content 2.37 48.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 308.21 α = 90 b = 103.62 β = 90 c = 95.75 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 2M 2022-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 2.45 49.16 100 0.195 0.212 0.081 0.996 12.9 13 113578
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 2.45 2.49 100 1.302 1.417 0.556 0.783 2.4 12.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.45 49.16 107681 5817 99.98 0.18743 0.18491 0.1918 0.23398 0.2373 RANDOM 37.955
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] -1.56 0.76 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.779 r_dihedral_angle_2_deg 9.585 r_dihedral_angle_1_deg 7.611 r_long_range_B_refined 5.775 r_long_range_B_other 5.773 r_scangle_other 4.725 r_mcangle_it 3.538 r_mcangle_other 3.538 r_scbond_it 3.173 r_scbond_other 3.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.779 r_dihedral_angle_2_deg 9.585 r_dihedral_angle_1_deg 7.611 r_long_range_B_refined 5.775 r_long_range_B_other 5.773 r_scangle_other 4.725 r_mcangle_it 3.538 r_mcangle_other 3.538 r_scbond_it 3.173 r_scbond_other 3.173 r_mcbond_it 2.382 r_mcbond_other 2.382 r_angle_refined_deg 2.342 r_angle_other_deg 0.786 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21858 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing