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Crystal Structure of Lectin from Pleurotus ostreatus in complex with GalNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 300 0.9M Na2HPO4/K2HPO4, pH 5.5, 33% glycerol
Crystal Properties Matthews coefficient Solvent content 6.26 80.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.273 α = 90 b = 152.273 β = 90 c = 145.975 γ = 120
Symmetry Space Group P 61 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 100 PIXEL DECTRIS EIGER2 X 16M Si 111. Rosenbaum-Rock double-crystal monochromator 2018-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.99 APS 22-ID
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 2.098 30 99.9 0.996 16.3 5 58637
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 2.1 2.18 0.996
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 3W5N 2.098 29.642 58628 2000 99.899 0.193 0.1927 0.2029 0.2055 0.2153 32.103
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] 0.006 0.003 0.006 -0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.148 r_dihedral_angle_4_deg 22.108 r_dihedral_angle_3_deg 12.688 r_dihedral_angle_1_deg 10.495 r_lrange_it 7.483 r_lrange_other 7.307 r_scangle_it 6.244 r_scangle_other 6.242 r_scbond_it 4.601 r_scbond_other 4.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.148 r_dihedral_angle_4_deg 22.108 r_dihedral_angle_3_deg 12.688 r_dihedral_angle_1_deg 10.495 r_lrange_it 7.483 r_lrange_other 7.307 r_scangle_it 6.244 r_scangle_other 6.242 r_scbond_it 4.601 r_scbond_other 4.6 r_mcangle_it 3.861 r_mcangle_other 3.86 r_mcbond_it 2.922 r_mcbond_other 2.921 r_angle_refined_deg 2.098 r_angle_other_deg 1.469 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.207 r_symmetry_nbd_other 0.198 r_symmetry_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.177 r_nbd_other 0.144 r_symmetry_xyhbond_nbd_other 0.101 r_metal_ion_refined 0.1 r_symmetry_nbtor_other 0.098 r_chiral_restr 0.089 r_symmetry_nbd_refined 0.069 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2505 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling BALBES phasing