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Joint X-ray/neutron room temperature structure of perdeuterated LecB lectin in complex with perdeuterated fucose
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GZT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.1 M Tris/DCl, pD 7.1, 20% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.26 45.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.9 α = 90 b = 73.87 β = 94.58 c = 55.003 γ = 90
Symmetry Space Group P 1 21 1
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 2020-09-16 M SINGLE WAVELENGTH 2 1 neutron 293 IMAGE PLATE LADI III 2020-08-18 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE Xenocs GeniX 3D Cu HF 1.5418 2 NUCLEAR REACTOR ILL BEAMLINE LADI III 2.8-3.8 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 1.85 33 96.6 0.097 1 11.3 7 34855 12.85 2 1.9 43 73.8 10.9 5.5 3.7 24478 12.85
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 1.85 1.89 0.85 2 1.9 2.08 17
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 1.85 27.41 1.36 34734 1736 96.22 0.1061 0.1042 0.1048 0.1419 0.1421 21.52 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.9 42.92 24283 1195 72.84 0.1941 0.1914 0.2461
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 17.8892 f_dihedral_angle_d 17.8892 f_angle_d 1.2693 f_angle_d 1.2693 f_chiral_restr 0.074 f_chiral_restr 0.074 f_bond_d 0.0101 f_bond_d 0.0101 f_plane_restr 0.0068 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3308 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 57
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Coot model building SCALA data scaling PHASER phasing