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Lipid-induced Conformational Switch Controls Fusion Activity of Longin Domain SNARE Ykt6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BW6 PDB ENTRY 3BW6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 2M (NH4)2SO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.97 37.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.81 α = 90 b = 59.71 β = 90 c = 108.33 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2008-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.443 30 100 0.067 10 5.1 6900 6788
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 2.443 2.506 100 0.336 2.2 5.2
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 THROUGHOUT PDB ENTRY 3BW6 2.443 30 6195 683 99.96 0.20516 0.1994 0.198 0.26137 0.2623 RANDOM 33.673
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] -0.49 1.11 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.731 r_dihedral_angle_3_deg 17.486 r_dihedral_angle_4_deg 14.732 r_dihedral_angle_1_deg 5.369 r_scangle_it 1.581 r_angle_refined_deg 1.06 r_scbond_it 0.98 r_mcangle_it 0.936 r_mcbond_it 0.605 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.731 r_dihedral_angle_3_deg 17.486 r_dihedral_angle_4_deg 14.732 r_dihedral_angle_1_deg 5.369 r_scangle_it 1.581 r_angle_refined_deg 1.06 r_scbond_it 0.98 r_mcangle_it 0.936 r_mcbond_it 0.605 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.222 r_nbd_refined 0.187 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.105 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1540 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 33
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling