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Room temperature X-ray structure of H/D-exchanged 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 0.4 M Na/K tartrate dissolved in D2O, soaked with 50 mM L-fucose dissolved in D2O
Crystal Properties Matthews coefficient Solvent content 3.08 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.6 α = 90 b = 89.24 β = 90 c = 159.28 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 293 CCD ADSC QUANTUM 315r 2018-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9796 ESRF BM30A
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 1.6 46 98.7 0.06 1 16.2 5.2 67576 19.77
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 1.6 1.64 0.7
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 1.6 39.82 1.35 67565 3378 98.7 0.151 0.1499 0.1478 0.1728 0.1711 22.55
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 4.1762 f_angle_d 0.8157 f_chiral_restr 0.0604 f_bond_d 0.0052 f_plane_restr 0.0048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2750 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing