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Beta-1,2-glucan-binding protein soaked with cyclic beta-1,2-glucoeicosaose
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-glucoeicosaose
Crystal Properties Matthews coefficient Solvent content 2.68 54.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.654 α = 90 b = 83.214 β = 90 c = 94.153 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 1.37 47.32 100 1 33 12.8 120251
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 1.37 1.39 100 0.906
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 1.37 47.316 120147 5953 99.967 0.169 0.1687 0.1775 0.1839 0.1937 18.38
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] 0.013 -0.006 -0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.029 r_dihedral_angle_6_deg 16.142 r_dihedral_angle_3_deg 12.451 r_dihedral_angle_1_deg 6.242 r_lrange_it 5.209 r_lrange_other 5.139 r_scangle_it 4.752 r_scangle_other 4.702 r_scbond_it 3.174 r_scbond_other 3.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.029 r_dihedral_angle_6_deg 16.142 r_dihedral_angle_3_deg 12.451 r_dihedral_angle_1_deg 6.242 r_lrange_it 5.209 r_lrange_other 5.139 r_scangle_it 4.752 r_scangle_other 4.702 r_scbond_it 3.174 r_scbond_other 3.147 r_mcangle_other 2.464 r_mcangle_it 2.456 r_angle_refined_deg 1.911 r_mcbond_it 1.785 r_mcbond_other 1.784 r_angle_other_deg 1.005 r_symmetry_nbd_refined 0.384 r_nbd_refined 0.337 r_nbd_other 0.28 r_symmetry_nbd_other 0.208 r_symmetry_xyhbond_nbd_refined 0.208 r_xyhbond_nbd_other 0.208 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.083 r_gen_planes_other 0.015 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3375 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 151
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing