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Crystal structure of GH97 glucodextranase from Flavobacterium johnsoniae in complex with glucose
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 2.37 48.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 307.927 α = 90 b = 103.691 β = 90 c = 95.671 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 PILATUS3 S 2M 2021-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.95 49.13 100 0.09 0.097 0.037 1 23 13.5 223030
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 1.95 1.98 99.9 1.471 1.588 0.594 0.836 2.2 13.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.95 49.13 222978 10922 99.975 0.191 0.189 0.1929 0.2289 0.2324 41.206
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] -3.013 3.232 -0.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.894 r_dihedral_angle_3_deg 15.167 r_dihedral_angle_2_deg 9.208 r_dihedral_angle_1_deg 7.51 r_lrange_it 5.923 r_lrange_other 5.922 r_scangle_it 4.783 r_scangle_other 4.783 r_mcangle_it 3.602 r_mcangle_other 3.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.894 r_dihedral_angle_3_deg 15.167 r_dihedral_angle_2_deg 9.208 r_dihedral_angle_1_deg 7.51 r_lrange_it 5.923 r_lrange_other 5.922 r_scangle_it 4.783 r_scangle_other 4.783 r_mcangle_it 3.602 r_mcangle_other 3.602 r_scbond_it 3.486 r_scbond_other 3.486 r_mcbond_it 2.785 r_mcbond_other 2.785 r_angle_refined_deg 1.902 r_angle_other_deg 0.632 r_nbd_other 0.219 r_nbd_refined 0.208 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.169 r_symmetry_nbd_refined 0.144 r_xyhbond_nbd_refined 0.137 r_metal_ion_refined 0.113 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.087 r_ncsr_local_group_1 0.073 r_ncsr_local_group_3 0.07 r_ncsr_local_group_4 0.07 r_ncsr_local_group_5 0.069 r_ncsr_local_group_6 0.064 r_ncsr_local_group_2 0.058 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21871 Nucleic Acid Atoms Solvent Atoms 848 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing