2ZII

Crystal Structure of Yeast Vps74-N-term Truncation Variant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZIHPDB ENTRY 2ZIH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629315% PEG 3350, 5% glycerol, 10mM citrate, 0.75mM KCl, 50mM EGTA, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.4664.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.081α = 90
b = 104.081β = 90
c = 292.759γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702007-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.91790CHESSF1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.055099.80.1425.66.13587249.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.053.161000.5296.23524

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2ZIH3.0549.135793179099.730.2230.220.281RANDOM42.122
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]
0.870.430.87-1.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.412
r_dihedral_angle_4_deg22.473
r_dihedral_angle_3_deg21.659
r_dihedral_angle_1_deg6.888
r_scangle_it2.395
r_angle_refined_deg1.663
r_scbond_it1.426
r_mcangle_it1.134
r_mcbond_it0.62
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.412
r_dihedral_angle_4_deg22.473
r_dihedral_angle_3_deg21.659
r_dihedral_angle_1_deg6.888
r_scangle_it2.395
r_angle_refined_deg1.663
r_scbond_it1.426
r_mcangle_it1.134
r_mcbond_it0.62
r_nbtor_refined0.32
r_nbd_refined0.244
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.18
r_symmetry_hbond_refined0.153
r_chiral_restr0.112
r_bond_refined_d0.014
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8588
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms

Software

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