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Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from XFEL diffraction
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N7S 1N7S, 3F04, 1UOW experimental model PDB 3F04 1N7S, 3F04, 1UOW experimental model PDB 1UOW 1N7S, 3F04, 1UOW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 5.45 77.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.386 α = 90 b = 170.676 β = 90 c = 291.014 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 RAYONIX MX-325 2014-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE XPP 1.307 SLAC LCLS XPP
Serial Crystallography Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 cryo-loop goniometer DCSS 100 mM Tris-HCl (pH 8.5), 1.5 M ammonium sulfate
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 40 (fs) 30 9 (KeV) 1
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 309 578 309
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 3.5 20 97.8 0.494 0.943 3.6 6.1 43622 66.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.56 89.2 0.795 0.2 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1N7S, 3F04, 1UOW 3.5 19.956 1.33 40510 2083 91.3 0.2939 0.292 0.2936 0.3291 0.3339 106
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 13.941 f_angle_d 0.45 f_chiral_restr 0.037 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10542 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 19
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction cctbx.xfel data reduction cctbx.prime data scaling PHASER phasing