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Crystal structure of CGL1 from Crassostrea gigas, mannobiose-bound form (CGL1/Man(alpha)1-2Man)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2 M magnesium acetate,
0.1 M sodium cacodylate (pH 6.5),
20% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.03 39.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.749 α = 90 b = 58.701 β = 93.701 c = 108.405 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 PIXEL DECTRIS PILATUS3 S 6M 2021-12-02 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) R Merge I (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 39.8 85.9 0.056 0.999 18.6 6.8 229413
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 1.02 0.872
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 39.778 229386 11557 85.767 0.175 0.1744 0.1833 0.1869 0.1945 10.872
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] -0.001 0.013 0.007 -0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.984 r_rigid_bond_restr 14.956 r_dihedral_angle_3_deg 12.517 r_dihedral_angle_1_deg 7.312 r_dihedral_angle_2_deg 4.519 r_lrange_it 2.767 r_lrange_other 2.767 r_angle_refined_deg 1.768 r_scangle_it 1.615 r_scangle_other 1.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.984 r_rigid_bond_restr 14.956 r_dihedral_angle_3_deg 12.517 r_dihedral_angle_1_deg 7.312 r_dihedral_angle_2_deg 4.519 r_lrange_it 2.767 r_lrange_other 2.767 r_angle_refined_deg 1.768 r_scangle_it 1.615 r_scangle_other 1.615 r_mcangle_it 1.466 r_mcangle_other 1.466 r_scbond_other 1.233 r_scbond_it 1.231 r_mcbond_it 1.095 r_mcbond_other 1.095 r_angle_other_deg 1.017 r_symmetry_nbd_refined 0.363 r_nbd_other 0.284 r_symmetry_nbd_other 0.209 r_nbd_refined 0.205 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.118 r_chiral_restr 0.107 r_symmetry_nbtor_other 0.106 r_gen_planes_other 0.016 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4360 Nucleic Acid Atoms Solvent Atoms 802 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing