☰ Navigation Tabs
Crystal structure of GH66 endodextranase from Flavobacterium johnsoniae in complex with isomaltotriose
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 2.03 39.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.911 α = 90 b = 91.058 β = 90 c = 137.354 γ = 90
Symmetry Space Group P 21 21 21
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 2022-05-15 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 1.18 45.78 99.9 0.063 0.069 0.019 1 19 12.5 173012
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 1.18 1.2 0.975 1.065 0.302 0.804 2.5
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.18 45.57 172910 8674 99.81 0.164 0.1626 0.1896 0.1836 14.527
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] -0.318 0.528 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.568 r_dihedral_angle_3_deg 13.328 r_dihedral_angle_2_deg 10.228 r_dihedral_angle_1_deg 7.268 r_rigid_bond_restr 3.339 r_angle_refined_deg 1.648 r_lrange_it 1.263 r_lrange_other 1.197 r_scangle_it 0.774 r_scangle_other 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.568 r_dihedral_angle_3_deg 13.328 r_dihedral_angle_2_deg 10.228 r_dihedral_angle_1_deg 7.268 r_rigid_bond_restr 3.339 r_angle_refined_deg 1.648 r_lrange_it 1.263 r_lrange_other 1.197 r_scangle_it 0.774 r_scangle_other 0.77 r_mcangle_it 0.696 r_mcangle_other 0.696 r_angle_other_deg 0.567 r_scbond_it 0.552 r_scbond_other 0.549 r_mcbond_it 0.474 r_mcbond_other 0.474 r_nbd_refined 0.25 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.18 r_nbd_other 0.158 r_xyhbond_nbd_refined 0.126 r_symmetry_nbd_refined 0.104 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.082 r_metal_ion_refined 0.076 r_symmetry_xyhbond_nbd_other 0.033 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4341 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing