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Crystal structure of an endosomal SNARE core complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SFC PDB ENTRY 1SFC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 PROTEIN SOLUTION: 20 MG/ML OF QUATERNARY COMPLEX IN 20MM TRIS-HCL AT PH 7.4 WELL SOLUTION: 0.1M NA-ACETATE AT PH 5.2, 2.5 M NA-FORMIAT, 15% GLYCEROL HANGING DROPS WITH 2MUL + 2 MUL
Crystal Properties Matthews coefficient Solvent content 30
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.7 α = 90 b = 41.1 β = 109.4 c = 51.5 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate COSMIC MIRRORS CMF12-38CU6 2001-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE SIEMENS M18X
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 15 93.7 0.0345 30.57 5.5 71259 14.3
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 1.9 2 88.8 0.137 11.35 4.6
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SFC 1.9 14.9 14797 737 92.7 0.176 0.176 0.224 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] 7.34 1.15 -2.53 -4.81
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 13.8 c_scangle_it 3.98 c_mcangle_it 2.58 c_scbond_it 1.71 c_mcbond_it 1.12 c_angle_deg 0.8 c_improper_angle_d 0.58 c_bond_d 0.004 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 13.8 c_scangle_it 3.98 c_mcangle_it 2.58 c_scbond_it 1.71 c_mcbond_it 1.12 c_angle_deg 0.8 c_improper_angle_d 0.58 c_bond_d 0.004 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1796 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling EPMR phasing