Navigation Tabs Neutron crystal structure of perdeuterated galectin-3C in complex with lactose
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 7.5 295 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 drops that was first equilibrated for 1 week. A 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. For details see Manzoni et al. (2016). 2 VAPOR DIFFUSION 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 drops that was first equilibrated for 1 week. A 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. For details see Manzoni et al. (2016).
Crystal Properties Matthews coefficient Solvent content 2.19 44 2.19 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.01 α = 90 b = 58.36 β = 90 c = 63.82 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 298 CCD MARMOSAIC 325 mm CCD FOCUSING MIRRORS 2015-05-31 M SINGLE WAVELENGTH 2 1 neutron 298 IMAGE PLATE LADI III 2014-12-15 L LAUE 3 1 neutron 298 AREA DETECTOR ORNL ANGER CAMERA 2015-05-15 L LAUE
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 ILL BEAMLINE LADI III 3.35-4.35 ILL LADI III 3 SPALLATION SOURCE ORNL Spallation Neutron Source BEAMLINE MANDI 2.0-4.0 ORNL Spallation Neutron Source MANDI
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 1.07 40 99.4 0.032 1 24.7 6.6 61354 2 1.7 28 95.8 0.209 0.052 22.2 13 15485 2 1.7 28 87.1 0.162 0.044 12.4 10 13741 3 1.6 19 81.3 0.155 0.066 12.2 4.4 15485
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 1.07 1.1 0.817 0.772 2.1 2 1.7 1.8 0.334 0.139 3.9 4.9 2 1.7 1.8 0.208 0.076 7 4.9 3 1.6 1.66 0.207 0.15 2.4 1.7
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 NEUTRON DIFFRACTION FOURIER SYNTHESIS 1.7 28 15194 769 96.2 0.17 0.168 0.211 X-RAY DIFFRACTION FOURIER SYNTHESIS 1.1 32 56662 2815 99.4 0.107 0.125 RANDOM
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 13.887 f_angle_d 1.735 f_chiral_restr 0.117 f_bond_d 0.011 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1104 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement LAUEGEN data reduction LSCALE data scaling SCALA data scaling Mantid data reduction XPREP data scaling PHENIX phasing