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Beta-1,2-glucan-binding protein complexed with cyclic beta-1,2-glucoheptadecaose
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-glucoheptadecaose
Crystal Properties Matthews coefficient Solvent content 2.66 53.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.389 α = 90 b = 82.908 β = 90 c = 94.071 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 1.95 47.18 98.5 0.997 12.8 12.4 41270
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 1.95 2 97.4 0.942
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 1.95 47.176 41091 1975 97.878 0.249 0.2472 0.2534 0.2836 0.2897 31.102
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] -0.07 0.039 0.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.723 r_dihedral_angle_3_deg 15.457 r_dihedral_angle_2_deg 8.757 r_dihedral_angle_1_deg 6.924 r_lrange_it 5.381 r_lrange_other 5.381 r_scangle_it 4.157 r_scangle_other 4.156 r_mcangle_it 3.254 r_mcangle_other 3.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.723 r_dihedral_angle_3_deg 15.457 r_dihedral_angle_2_deg 8.757 r_dihedral_angle_1_deg 6.924 r_lrange_it 5.381 r_lrange_other 5.381 r_scangle_it 4.157 r_scangle_other 4.156 r_mcangle_it 3.254 r_mcangle_other 3.254 r_scbond_it 2.797 r_scbond_other 2.796 r_mcbond_it 2.393 r_mcbond_other 2.393 r_angle_refined_deg 1.477 r_angle_other_deg 0.829 r_nbd_refined 0.373 r_nbd_other 0.259 r_xyhbond_nbd_other 0.227 r_symmetry_nbd_other 0.226 r_xyhbond_nbd_refined 0.209 r_symmetry_nbd_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.199 r_nbtor_refined 0.189 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.07 r_gen_planes_other 0.008 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3358 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 193
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing