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Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (short unit cell form)
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 4.56 73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.073 α = 90 b = 171.626 β = 90 c = 146.942 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2014-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (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 3.6 50 99.7 0.067 0.105 0.027 4 14.5 20922 133.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.6 3.73 98.7 0.741 0.948 0.252 0.895 12.4 2017
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1N7S,3F04,1UOW 3.6 48.29 1.37 20850 1085 99.4 0.251 0.249 0.289 0.2743 157.7
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 11.227 f_angle_d 0.862 f_chiral_restr 0.04 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6321 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 7
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing