Navigation Tabs Neutron crystal structure of perdeuterated galectin-3C in complex with glycerol
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZSJ
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 introduced. The drop was fed with fresh protein by adding 3-4 micro litres of protein with 10 mM lactose every 3-4 days for 3 months. Then the lactose was exchanged for glycerol by dialysis for at least one month against 10% glycerol (1.37 M), 24% PEG 4000 in the same buffer. For details see Manzoni et al. (2016).
Crystal Properties Matthews coefficient Solvent content 2.19 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.314 α = 90 b = 58.352 β = 90 c = 63.867 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 MARMOSAIC 225 mm CCD 2016-05-15 M SINGLE WAVELENGTH 2 1 neutron 298 IMAGE PLATE BIODIFF 2015-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0000 MAX II I911-3 2 NUCLEAR REACTOR FRM II BEAMLINE BIODIFF 2.67 FRM II BIODIFF
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 1.1 43.1 95 0.068 0.02 1 20.2 12.3 54414 11.45 2 1.65 28.2 94.7 0.135 0.087 5.9 3.1 16592 11.45
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 1.1 1.12 1.259 0.543 0.726 1.4 7 2 1.65 1.71 0.499 1.6 2.6
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 1.1 31.93 1.34 54347 2751 94.79 0.1239 0.1231 0.12 0.1373 0.14 15.31 NEUTRON DIFFRACTION FOURIER SYNTHESIS 1.7 28.2 15178 782 95.3 0.1522 0.1502 0.1873
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 17.6582 f_angle_d 1.7351 f_chiral_restr 0.1292 f_bond_d 0.0097 f_plane_restr 0.0081
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1106 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction XDS data reduction Aimless data scaling PHENIX phasing
