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crystal structure of Pholiota squarrosa lectin in complex with a dodecasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other PhoslOcta
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 292 3.4 M Na malonate pH5
Crystal Properties Matthews coefficient Solvent content 2.39 48.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.744 α = 90 b = 101.744 β = 90 c = 101.744 γ = 90
Symmetry Space Group I 21 3
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 PILATUS 6M 2017-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9793 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 41.54 100 0.05 0.018 1 32.8 17.3 19409
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 100 0.663 0.239 0.917 4.6 16.9
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 PhoslOcta 1.7 41 18434 973 99.95 0.15883 0.15733 0.1673 0.18661 0.1962 RANDOM 26.598
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.792 r_dihedral_angle_4_deg 10.2 r_dihedral_angle_3_deg 9.193 r_dihedral_angle_1_deg 7.214 r_long_range_B_refined 6.519 r_long_range_B_other 6.103 r_scangle_other 4.508 r_scbond_it 2.968 r_scbond_other 2.963 r_mcangle_other 2.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.792 r_dihedral_angle_4_deg 10.2 r_dihedral_angle_3_deg 9.193 r_dihedral_angle_1_deg 7.214 r_long_range_B_refined 6.519 r_long_range_B_other 6.103 r_scangle_other 4.508 r_scbond_it 2.968 r_scbond_other 2.963 r_mcangle_other 2.513 r_mcangle_it 2.512 r_angle_refined_deg 2.064 r_mcbond_it 1.705 r_mcbond_other 1.688 r_angle_other_deg 0.964 r_chiral_restr 0.111 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 648 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 241
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing