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Pholiota squarrosa lectin (PhoSL) in complex with fucose(alpha1-6)[GlcNAc(beta1-4)]GlcNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6A86
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 4.3 M sodium formate (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.98 58.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.739 α = 90 b = 127.057 β = 90 c = 39.418 γ = 90
Symmetry Space Group C 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER X 16M 2019-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0 Photon Factory BL-17A
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 2.154 44.87 99.5 0.087 0.996 9.18 3.5 17730
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 2.154 2.28 99.3 0.661 0.684 1.81 3.43
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6A86 2.154 44.865 17729 887 99.842 0.182 0.1788 0.1853 0.2446 0.2492 38.896
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] 0.064 -0.041 -0.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.7 r_dihedral_angle_other_3_deg 26.075 r_dihedral_angle_1_deg 18.712 r_dihedral_angle_3_deg 16.832 r_lrange_other 7.943 r_lrange_it 7.923 r_scangle_it 6.243 r_scangle_other 6.242 r_mcangle_it 5.139 r_mcangle_other 5.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.7 r_dihedral_angle_other_3_deg 26.075 r_dihedral_angle_1_deg 18.712 r_dihedral_angle_3_deg 16.832 r_lrange_other 7.943 r_lrange_it 7.923 r_scangle_it 6.243 r_scangle_other 6.242 r_mcangle_it 5.139 r_mcangle_other 5.138 r_scbond_other 4.208 r_scbond_it 4.206 r_mcbond_it 3.326 r_mcbond_other 3.324 r_angle_refined_deg 1.774 r_angle_other_deg 1.21 r_symmetry_xyhbond_nbd_refined 0.271 r_nbd_other 0.249 r_symmetry_nbd_refined 0.197 r_nbd_refined 0.192 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.153 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1878 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 252
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing