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The structure of cyclization domain in cyclic beta-1,2-glucan synthase from Thermoanaerobacter italicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other We used the cyclization domain structure from the full-length predicted structure of cyclic beta-1,2-glucan synthase generated by alphafold2 for molecular replacement
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M sodium cacodylate, 1.3M sodium acetate
Crystal Properties Matthews coefficient Solvent content 5.3 76.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.719 α = 90 b = 172.719 β = 90 c = 395.599 γ = 90
Symmetry Space Group P 41 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 6M 2021-10-23 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) 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 3.9 89.6 100 0.992 9.8 25 55512
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.9 4.01 0.851
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.9 89.6 52696 2738 99.96 0.19991 0.19819 0.2042 0.23237 0.2317 RANDOM
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] -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.536 r_dihedral_angle_3_deg 22.671 r_dihedral_angle_4_deg 20.887 r_long_range_B_refined 20.288 r_long_range_B_other 20.288 r_scangle_other 14.884 r_mcangle_it 14.251 r_mcangle_other 14.251 r_mcbond_it 9.073 r_mcbond_other 9.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.536 r_dihedral_angle_3_deg 22.671 r_dihedral_angle_4_deg 20.887 r_long_range_B_refined 20.288 r_long_range_B_other 20.288 r_scangle_other 14.884 r_mcangle_it 14.251 r_mcangle_other 14.251 r_mcbond_it 9.073 r_mcbond_other 9.067 r_scbond_it 8.95 r_scbond_other 8.948 r_dihedral_angle_1_deg 6.881 r_angle_refined_deg 1.597 r_angle_other_deg 1.167 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18842 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement BUCCANEER model building MOLREP phasing Aimless data scaling XDS data reduction