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Crystal structure of perdeuterated PLL lectin in complex with L-fucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C9O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Na/K tartrate dissolved in D2O, co-crystallized with 50 mM L-fucose dissolved in D2O
Crystal Properties Matthews coefficient Solvent content 3.03 59.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.839 α = 90 b = 88.302 β = 90 c = 158.331 γ = 90
Symmetry Space Group I 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 100 PIXEL DECTRIS PILATUS 6M 2018-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972 ESRF ID23-1
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 1.7 56 98 0.1 0.99 7.9 4.2 55209 15.7
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 1.7 1.73 0.36 0.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5c9o 1.7 45.82 1.36 55114 2785 97.61 0.1731 0.1717 0.1764 0.1993 0.2033 19.57
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 f_dihedral_angle_d 3.6034 f_angle_d 0.8792 f_chiral_restr 0.0582 f_bond_d 0.006 f_plane_restr 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2750 Nucleic Acid Atoms Solvent Atoms 593 Heterogen Atoms 131
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing