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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.14 0.1541 0.15 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
