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Crystal structure of GH66 endodextranase from Flavobacterium johnsoniae
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 2.17 43.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.241 α = 90 b = 48.409 β = 104.601 c = 76.453 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 1.85 47.3 99.7 0.112 0.134 0.073 0.995 10.1 6.3 47439
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 1.85 1.89 0.875 1.033 0.546 0.87 1.9
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 1.85 47.3 47428 2332 99.637 0.177 0.1748 0.1839 0.2304 0.2379 32.254
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] 1.714 -0.286 -0.5 -0.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.138 r_dihedral_angle_3_deg 14.865 r_dihedral_angle_1_deg 8.294 r_lrange_it 5.783 r_lrange_other 5.766 r_dihedral_angle_2_deg 5.722 r_scangle_it 3.902 r_scangle_other 3.901 r_scbond_it 2.809 r_scbond_other 2.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.138 r_dihedral_angle_3_deg 14.865 r_dihedral_angle_1_deg 8.294 r_lrange_it 5.783 r_lrange_other 5.766 r_dihedral_angle_2_deg 5.722 r_scangle_it 3.902 r_scangle_other 3.901 r_scbond_it 2.809 r_scbond_other 2.808 r_mcangle_it 2.546 r_mcangle_other 2.546 r_angle_refined_deg 2.151 r_mcbond_it 1.927 r_mcbond_other 1.926 r_angle_other_deg 0.748 r_nbd_refined 0.219 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.193 r_symmetry_nbd_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.168 r_nbd_other 0.159 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.113 r_symmetry_nbtor_other 0.089 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 4341 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing