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Crystal structure of GH66 endodextranase from Flavobacterium johnsoniae in complex with isomaltose
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 2.11 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.712 α = 90 b = 47.996 β = 104.64 c = 76.477 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 46.9 99.7 0.121 0.144 0.077 0.997 11 6.7 50250
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 0.92 1.085 0.57 0.839 2.3
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 46.9 50249 2536 99.679 0.21 0.2083 0.2035 0.2527 0.2478 28.622
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] -1.337 0.696 0.752 0.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.051 r_dihedral_angle_3_deg 14.477 r_dihedral_angle_1_deg 7.8 r_lrange_other 5.62 r_lrange_it 5.608 r_dihedral_angle_2_deg 4.314 r_angle_refined_deg 1.501 r_scangle_it 1.369 r_scangle_other 1.369 r_mcangle_it 0.975
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.051 r_dihedral_angle_3_deg 14.477 r_dihedral_angle_1_deg 7.8 r_lrange_other 5.62 r_lrange_it 5.608 r_dihedral_angle_2_deg 4.314 r_angle_refined_deg 1.501 r_scangle_it 1.369 r_scangle_other 1.369 r_mcangle_it 0.975 r_mcangle_other 0.975 r_scbond_other 0.917 r_scbond_it 0.915 r_mcbond_it 0.707 r_mcbond_other 0.707 r_angle_other_deg 0.51 r_nbd_refined 0.225 r_symmetry_nbd_other 0.203 r_nbd_other 0.19 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_refined 0.11 r_metal_ion_refined 0.086 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.073 r_symmetry_nbd_refined 0.065 r_symmetry_xyhbond_nbd_other 0.012 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4398 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing