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Crystal structure of GH97 glucodextranase mutant E509Q from Flavobacterium johnsoniae in complex with panose
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 293 12% PEG20000, 200 mM sodium cacodylate buffer (pH 6.0), 200 mM magnesium acetate, 10 mM glucose
Crystal Properties Matthews coefficient Solvent content 2.42 49.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 290.693 α = 90 b = 102.708 β = 90 c = 104.529 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 2.34 49.23 100 0.21 0.227 0.086 0.997 11.7 13.2 132638
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 2.34 2.38 100 1.347 1.453 0.542 0.734 2.1 13.8
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 2.34 49.23 125898 6575 99.92 0.21057 0.20827 0.2133 0.25445 0.2586 RANDOM 34.213
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] 0.54 0.78 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.064 r_dihedral_angle_2_deg 10.44 r_dihedral_angle_1_deg 7.822 r_long_range_B_refined 5.658 r_long_range_B_other 5.654 r_scangle_other 4.64 r_mcangle_it 3.875 r_mcangle_other 3.875 r_scbond_it 3.203 r_scbond_other 3.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.064 r_dihedral_angle_2_deg 10.44 r_dihedral_angle_1_deg 7.822 r_long_range_B_refined 5.658 r_long_range_B_other 5.654 r_scangle_other 4.64 r_mcangle_it 3.875 r_mcangle_other 3.875 r_scbond_it 3.203 r_scbond_other 3.203 r_mcbond_it 2.748 r_mcbond_other 2.748 r_angle_refined_deg 2.078 r_angle_other_deg 0.695 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 21902 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing