Navigation Tabs Neutron crystal structure of perdeuterated galectin-3C in the ligand-free form
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 12-15% PEG 4000 OR PEG 3000, 0.1M MGCL2, 0.015M BETA MERCAPTOETHANOL, 0.1M TRIS-DCL, PD 7.9, 0.4M NASCN. ALL DISSOLVED IN D2O. CRYSTAL GROWN IN A 15 + 15 MICROLITRE SITTING DROP THAT WAS FIRST EQUILIBRATED FOR 1 WEEK. A SMALL CRYSTAL GROWN AT 20-28% PEG WAS THEN INTRODUCED. THE DROP WAS FED WITH FRESH PROTEIN BY ADDING 3-4 MICROLITRES OF PROTEIN WITH 10 MM LACTOSE EVERY 3-4 DAYS FOR 3 MONTHS. LACTOSE WAS THEN REMOVED IN TWO STEPS, FIRST BY DIALYSING AGAINST 1M GLYCEROL FOR 1 MONTH THEN AGAINST BUFFER WITH NO GLYCEROL FOR 1 MONTH. FOR DETAILS, SEE MANZONI ET AL. (2016).
Crystal Properties Matthews coefficient Solvent content 2.19 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.39 α = 90 b = 58.62 β = 90 c = 64.02 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r FOCUSING MIRRORS 2017-03-10 M SINGLE WAVELENGTH 2 1 neutron 298 IMAGE PLATE 2017-02-15 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.98081 ESRF BM30A 2 NUCLEAR REACTOR ILL BEAMLINE LADI III 3.35-4.35 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 1.03 28 99.8 0.044 0.012 1 35.5 14 70173 2 1.8 30 83.8 0.132 0.053 0.993 8.5 4.9 9844
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 1.03 1.06 2.357 0.933 0.355 1 9.3 2 1.8 1.9 0.194 0.091 0.917 3.4
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 R-Free R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS 1.03 29.31 1.35 70165 4369 99.82 0.1384 0.1373 0.1541 NEUTRON DIFFRACTION FOURIER SYNTHESIS 1.757 28.094 11785 735 80.83 0.1741 0.1715 0.2107
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 16.358 f_dihedral_angle_d 16.358 f_angle_d 1.43 f_angle_d 1.43 f_chiral_restr 0.107 f_chiral_restr 0.107 f_bond_d 0.011 f_bond_d 0.011 f_plane_restr 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1108 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction LAUEGEN data scaling PHENIX phasing