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Structure of a fucose lectin from Kordia zhangzhouensis in complex with methyl-fucoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SAD model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 Morpheus 1 box 1 solution 40 for Mefuc complex or 35% PEG smear medium 10% isopropanol for complex with selenofucoside
Crystal Properties Matthews coefficient Solvent content 2.94 58.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.102 α = 90 b = 90.522 β = 90 c = 143.777 γ = 90
Symmetry Space Group P 2 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 PILATUS3 S 6M 2018-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.55 39.25 99.8 0.041 0.051 0.031 0.999 16.9 5 165158 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.57 98 0.654 0.824 0.496 0.773 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT SAD model 1.55 39.25 156839 8260 99.72 0.15659 0.15536 0.1685 0.18002 0.1914 RANDOM 21.131
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] -0.78 -0.5 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.365 r_dihedral_angle_3_deg 11.379 r_dihedral_angle_4_deg 7.667 r_dihedral_angle_1_deg 6.592 r_long_range_B_refined 5.122 r_long_range_B_other 5.121 r_scangle_other 3.716 r_scbond_it 2.656 r_scbond_other 2.656 r_mcangle_it 2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.365 r_dihedral_angle_3_deg 11.379 r_dihedral_angle_4_deg 7.667 r_dihedral_angle_1_deg 6.592 r_long_range_B_refined 5.122 r_long_range_B_other 5.121 r_scangle_other 3.716 r_scbond_it 2.656 r_scbond_other 2.656 r_mcangle_it 2.48 r_mcangle_other 2.479 r_mcbond_it 1.805 r_mcbond_other 1.803 r_angle_refined_deg 1.802 r_angle_other_deg 1.624 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6824 Nucleic Acid Atoms Solvent Atoms 1287 Heterogen Atoms 309
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling SHELXD phasing