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Crystal structure of GH66 endodextranase from Flavobacterium johnsoniae in complex with glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold ABQ07435.1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100mM Tris-HCl, pH 8.5-9.0, 200mM lithium sulfate, 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.15 42.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.181 α = 90 b = 48.381 β = 104.405 c = 76.487 γ = 90
Symmetry Space Group C 1 2 1
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 2022-03-05 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 1.8 47.26 98.3 0.132 0.156 0.083 0.997 10.3 6.7 50429
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 1.8 1.84 0.963 1.133 0.591 0.854 2.1
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 1.8 47.256 50428 2464 98.258 0.209 0.2061 0.2112 0.2593 0.263 27.053
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] 2.111 1.288 -0.833 -1.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.033 r_dihedral_angle_3_deg 14.967 r_dihedral_angle_2_deg 12.146 r_dihedral_angle_1_deg 7.964 r_lrange_other 4.486 r_lrange_it 4.483 r_scangle_it 2.508 r_scangle_other 2.507 r_angle_refined_deg 2.165 r_scbond_it 1.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.033 r_dihedral_angle_3_deg 14.967 r_dihedral_angle_2_deg 12.146 r_dihedral_angle_1_deg 7.964 r_lrange_other 4.486 r_lrange_it 4.483 r_scangle_it 2.508 r_scangle_other 2.507 r_angle_refined_deg 2.165 r_scbond_it 1.682 r_scbond_other 1.682 r_mcangle_it 1.532 r_mcangle_other 1.532 r_mcbond_it 1.049 r_mcbond_other 1.049 r_angle_other_deg 0.72 r_nbd_refined 0.215 r_nbd_other 0.208 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.173 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.106 r_symmetry_nbd_refined 0.093 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.022 r_gen_planes_refined 0.016 r_bond_refined_d 0.015 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4353 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing