☰ Navigation Tabs
Crystal Structure of a Complex Between the SNARE Nyv1 and the HOPS Vps33-Vps16 subcomplex from Chaetomium thermophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 TRIS-HCl buffer, 0.8M Na Tartrate, 0.5% w/v PEG 5000 monomethyl ether
Crystal Properties Matthews coefficient Solvent content 4.58 73.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.03 α = 90 b = 258.936 β = 90 c = 75.274 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 CCD ADSC QUANTUM 315r 2014-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 3.05 50 99.9 0.08 8.3 7.2 38474 -3 82
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 3.05 3.1 98.2 0.778 6.8 1828
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4KMO 3.1 49.466 1.34 36709 1877 99.87 0.1974 0.1948 0.199 0.2461 0.2458 Random selection 5% 116.1143
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 15.136 f_angle_d 1.065 f_chiral_restr 0.044 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6659 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction CBASS data collection DENZO data reduction