Navigation Tabs Structure of galectin-3C in complex with lactose determined by serial crystallography using an XtalTool support
Serial Crystallography (SX)
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, HANGING DROP 7.5 277 Crystals were grown on an XtalTool support (Jena Bioscience) over a 24 well VDX-plate with 1 ml reservoir. The drop consisted of 1 microlitre 20 mg/ml protein in 10 mM sodium phosphate pH 7.4, 100 mM NaCl, 10 mM beta-mercaptoethanol, 2 mM lactose), 0.25 microlitre of seed crystals in a stabilization solution containing 0.1 M Tris pH 7.5, 33% (w/v) PEG 4000, 0.1 M MgCl2, 0.2 M NaSCN) and 0.75 microlitre reservoir solution containing 0.1 M Tris pH 7.5, 30% PEG 4000, 0.05 M MgCl2, 0.2 M NaSCN and 8 mM beta-mercaptoethanol.
Crystal Properties Matthews coefficient Solvent content 2.16 43.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.66 α = 90 b = 58.05 β = 90 c = 63.72 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 PIXEL DECTRIS EIGER X 16M 2019-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9800 MAX IV BioMAX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 XtalTool (Jena Bioscience) fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 Crystallized directly on XtalTool SPINE pin MD3 (Arinax)
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 undefined (fs) undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 15555 15555
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.7 60 99.9 0.9589303 0.141 5.66 139 15552 17.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.75 0.7462656 0.37 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 FREE R-VALUE 6EYM 1.7 42.91 15137 1525 97.47 0.1484 0.1448 0.16 0.1806 0.19 RANDOM 22.1
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 13.7632 f_angle_d 0.8772 f_chiral_restr 0.0611 f_bond_d 0.0072 f_plane_restr 0.0059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1103 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement CrystFEL data reduction CrystFEL data scaling PHENIX phasing
