Navigation Tabs Structure of galectin-3C in complex with lactose determined by serial crystallography using a silicon nitride membrane 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 XtalTool supports (Jena Bioscience) over a 24 well VDX-plate with 1 ml reservoir. The drop was made up 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 microlitres of galectin-3C 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 microlitres reservoir solution containing 0.1 M Tris pH 7.5, 34% (w/v) PEG 4000, 0.2 M NaSCN and 8 mM beta-mercapthoethanol. Crystals grew to a size of approximately 10-15 micrometer.
Crystal Properties Matthews coefficient Solvent content 1.96 37.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.67 α = 90 b = 56.36 β = 90 c = 61.17 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 2019-04-04 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 silicon nitride membrane (Silson) fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 silicon nitride membrane cryo cap 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 13522 13522
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 61 100 0.155 5.3 195.2 14154 21.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.75 100 1.833 1.41 133.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6EYM 1.7 41.45 13586 678 96.29 0.1672 0.1656 0.17 0.197 0.2 28.49
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 13.0291 f_angle_d 1.5933 f_chiral_restr 0.0636 f_bond_d 0.0199 f_plane_restr 0.0085
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1106 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling PHENIX phasing
