X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YZQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3647.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.836α = 90
b = 75.95β = 98.44
c = 106.618γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9786SLSX10SA

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
11.952099.267917673783.819.16

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 REPLACEMENTTHROUGHOUT1YZQ1.9519.9663957338899.280.204410.202290.24428RANDOM36.651
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]
1.04-0.20.56-1.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.63
r_dihedral_angle_4_deg16.237
r_dihedral_angle_3_deg15.796
r_dihedral_angle_1_deg6.146
r_mcbond_other4.325
r_angle_other_deg4.199
r_scangle_it3.299
r_mcangle_it2.964
r_scbond_it2.08
r_mcbond_it1.904
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.63
r_dihedral_angle_4_deg16.237
r_dihedral_angle_3_deg15.796
r_dihedral_angle_1_deg6.146
r_mcbond_other4.325
r_angle_other_deg4.199
r_scangle_it3.299
r_mcangle_it2.964
r_scbond_it2.08
r_mcbond_it1.904
r_angle_refined_deg1.354
r_symmetry_vdw_refined0.308
r_symmetry_hbond_refined0.26
r_nbd_other0.241
r_symmetry_vdw_other0.24
r_nbd_refined0.223
r_xyhbond_nbd_refined0.194
r_nbtor_refined0.183
r_nbtor_other0.112
r_metal_ion_refined0.099
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_other0.005
r_gen_planes_refined0.004
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6273
Nucleic Acid Atoms
Solvent Atoms453
Heterogen Atoms145

Software

Software
Software NamePurpose
MOSFLMdata reduction
PHASESphasing
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling