3EIE

Crystal Structure of S.cerevisiae Vps4 in the SO4-bound state


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52961.6M Ammonium sulfate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
4.1870.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.83α = 90
b = 110.83β = 90
c = 169.12γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.0NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.73399.80.1090.09817628
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.899.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.73315893115297.490.244020.244020.2410.28701RANDOM43.671
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]
-0.76-0.38-0.761.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.176
r_dihedral_angle_3_deg19.984
r_dihedral_angle_4_deg18.695
r_dihedral_angle_1_deg6.347
r_scangle_it2.509
r_angle_refined_deg1.489
r_scbond_it1.413
r_mcangle_it1.105
r_mcbond_it0.583
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.176
r_dihedral_angle_3_deg19.984
r_dihedral_angle_4_deg18.695
r_dihedral_angle_1_deg6.347
r_scangle_it2.509
r_angle_refined_deg1.489
r_scbond_it1.413
r_mcangle_it1.105
r_mcbond_it0.583
r_chiral_restr0.105
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2351
Nucleic Acid Atoms
Solvent Atoms35
Heterogen Atoms10

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling