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Beta-1,2-glucan-binding protein complexed with cyclc beta-1,2-glucononadecaose
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-glucononadecaose
Crystal Properties Matthews coefficient Solvent content 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.488 α = 90 b = 83.197 β = 90 c = 94.235 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 1.27 47.28 100 1 35.6 12.8 150304
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 1.27 1.29 100 0.907
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 1.27 47.278 150194 7517 99.977 0.166 0.1652 0.1746 0.1807 0.1882 16.812
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] 0.012 -0.002 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.969 r_dihedral_angle_3_deg 12.717 r_dihedral_angle_2_deg 11.91 r_dihedral_angle_1_deg 6.211 r_lrange_it 4.798 r_lrange_other 4.732 r_scangle_it 4.236 r_scangle_other 4.21 r_scbond_it 2.894 r_scbond_other 2.879
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.969 r_dihedral_angle_3_deg 12.717 r_dihedral_angle_2_deg 11.91 r_dihedral_angle_1_deg 6.211 r_lrange_it 4.798 r_lrange_other 4.732 r_scangle_it 4.236 r_scangle_other 4.21 r_scbond_it 2.894 r_scbond_other 2.879 r_mcangle_other 2.173 r_mcangle_it 2.169 r_angle_refined_deg 1.92 r_mcbond_it 1.559 r_mcbond_other 1.559 r_angle_other_deg 1.028 r_nbd_refined 0.399 r_nbd_other 0.251 r_symmetry_nbd_refined 0.245 r_symmetry_nbd_other 0.213 r_symmetry_xyhbond_nbd_refined 0.202 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.17 r_xyhbond_nbd_other 0.132 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.013 r_gen_planes_other 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 3376 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 237
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing