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Crystal structure of CGL1 from Crassostrea gigas, mannotriose-bound form (CGL1/Man(alpha)1-2Man(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% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.04 39.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.734 α = 90 b = 58.674 β = 93.657 c = 108.41 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 0.97 39.771 100 0.036 1 28.6 12.8 292966
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.97 0.99 1.021 0.82
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 0.97 39.771 292928 14810 99.988 0.176 0.1751 0.185 0.1885 0.1969 11.064
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 -0.001 0.015 -0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.915 r_rigid_bond_restr 15.562 r_dihedral_angle_3_deg 12.802 r_dihedral_angle_1_deg 7.24 r_dihedral_angle_2_deg 4.098 r_lrange_it 3.374 r_lrange_other 3.341 r_scangle_it 2.931 r_scangle_other 2.931 r_scbond_other 2.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.915 r_rigid_bond_restr 15.562 r_dihedral_angle_3_deg 12.802 r_dihedral_angle_1_deg 7.24 r_dihedral_angle_2_deg 4.098 r_lrange_it 3.374 r_lrange_other 3.341 r_scangle_it 2.931 r_scangle_other 2.931 r_scbond_other 2.929 r_scbond_it 2.928 r_mcangle_it 2.221 r_mcangle_other 2.221 r_mcbond_it 2.142 r_mcbond_other 2.142 r_angle_refined_deg 1.799 r_angle_other_deg 0.993 r_symmetry_nbd_refined 0.296 r_nbd_other 0.251 r_symmetry_nbd_other 0.212 r_nbd_refined 0.211 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.119 r_symmetry_nbtor_other 0.107 r_chiral_restr 0.099 r_gen_planes_other 0.022 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4360 Nucleic Acid Atoms Solvent Atoms 815 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing