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X-ray Structure of the WD40 domain of HOPS subunit Vps11 from Yeast
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100 mM Tris pH 7.5, 11% PEG 6000, 3% glycerol, 0.5 mM TCEP. Cryoprotected with 30% glycerol supplementing the crystallization conditions.
Crystal Properties Matthews coefficient Solvent content 2.68 54.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.084 α = 90 b = 113.159 β = 90 c = 129.758 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 ADSC QUANTUM 315 2012-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.743 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 2.22 50 96.2 0.09 7.5 6.9 62899
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 2.22 2.26 85.5 0.928 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.22 47.76 61299 2985 93.83 0.1773 0.1745 0.1743 0.2341 0.2341 44.91
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 16.6358 f_angle_d 0.8926 f_chiral_restr 0.0609 f_bond_d 0.0072 f_plane_restr 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7853 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling SHELXCD phasing PDB_EXTRACT data extraction