2EQB

Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.2293150mM Dipotassium hydrogenphosphate, 17% PEG 3350, 150mM dimethyl(2-hydroxyethyl)ammonium propane sulfonate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
575.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.581α = 90
b = 117.422β = 90
c = 123.332γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-12-12MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 3152006-12-21MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-8BL41XU
2SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A0.97956, 0.97973Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1,22.75012.7236192361927.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.72.750.2882.07

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.748.0823220112198.20.2730.2730.298RANDOM77.7
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]
-20.940.93-20.02
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.2
c_scangle_it5.91
c_mcangle_it4.92
c_scbond_it3.65
c_mcbond_it2.83
c_angle_deg1.5
c_improper_angle_d0.75
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.2
c_scangle_it5.91
c_mcangle_it4.92
c_scbond_it3.65
c_mcbond_it2.83
c_angle_deg1.5
c_improper_angle_d0.75
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2899
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms10

Software

Software
Software NamePurpose
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing