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Beta-1,2-glucan-binding protein soaked with cyclic beta-1,2-glucooctaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 22HH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 ammonium sulfate, bis-Tris, cyclic beta-1,2-glucooctaose
Crystal Properties Matthews coefficient Solvent content 2.67 53.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.699 α = 90 b = 82.849 β = 90 c = 94.099 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 6M 2023-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 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 1.6 47.25 100 1 33.9 12.4 75627
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 1.6 1.63 99.9 0.946
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 1.6 35.992 75525 3838 99.938 0.168 0.1668 0.1796 0.1813 0.1924 20.339
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] 0.014 -0.005 -0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.037 r_dihedral_angle_2_deg 15.064 r_dihedral_angle_3_deg 12.756 r_dihedral_angle_1_deg 6.156 r_lrange_it 5.655 r_lrange_other 5.655 r_scangle_it 5.259 r_scangle_other 5.169 r_scbond_it 3.586 r_scbond_other 3.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.037 r_dihedral_angle_2_deg 15.064 r_dihedral_angle_3_deg 12.756 r_dihedral_angle_1_deg 6.156 r_lrange_it 5.655 r_lrange_other 5.655 r_scangle_it 5.259 r_scangle_other 5.169 r_scbond_it 3.586 r_scbond_other 3.535 r_mcangle_other 2.627 r_mcangle_it 2.622 r_mcbond_it 1.981 r_mcbond_other 1.981 r_angle_refined_deg 1.912 r_angle_other_deg 1.042 r_nbd_refined 0.325 r_symmetry_nbd_other 0.214 r_nbd_other 0.214 r_symmetry_nbd_refined 0.2 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.144 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.084 r_gen_planes_other 0.019 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_symmetry_xyhbond_nbd_other 0.01 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3375 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 163
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing