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Joint X-ray/neutron room temperature structure of perdeuterated PLL lectin in complex with perdeuterated L-fucose
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
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 0.1 M Na/K tartrate dissolved in D2O, soaked with 50 mM perdeuterated fucose-d12 dissolved in D2O
Crystal Properties Matthews coefficient Solvent content 3.08 60.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.665 α = 90 b = 89.21 β = 90 c = 159.235 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 IMAGE PLATE MAR scanner 345 mm plate 2020-01-15 M SINGLE WAVELENGTH 2 1 neutron 293 IMAGE PLATE LADI III 2019-08-04 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE Xenocs GeniX 3D Cu HF 1.542 2 NUCLEAR REACTOR ILL BEAMLINE LADI III 3.07-4.05 ILL LADI III
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.84 33 100 0.11 1 14.7 11.5 45276 19.08 2 2.2 46 84.9 0.16 8 4.1 22348 19.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.88 0.58 0.83 2 2.2 2.32 0.33
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.84 33 1.37 45271 2265 99.97 0.1222 0.1213 0.1223 0.1398 0.1409 34.65 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.2 45.99 22233 1112 83.26 0.1906 0.2211 34.65
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 13.9607 f_dihedral_angle_d 13.9607 f_angle_d 1.3225 f_angle_d 1.3225 f_chiral_restr 0.0743 f_chiral_restr 0.0743 f_bond_d 0.0103 f_bond_d 0.0103 f_plane_restr 0.0072 f_plane_restr 0.0072
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2750 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 66
Software Software Software Name Purpose PHENIX refinement iMOSFLM data processing Aimless data scaling SCALA data scaling PHENIX phasing LAUEGEN data processing LAUEGEN data reduction LSCALE data scaling