X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.6293Nucleotide-free Rab8a1 184:Rabin8157-232 was crystallized in 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6. Before data collection, the complex crystal was protected with cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6). In order to produce nucleotide-bound forms of Rab8:Rabin8 complexes, the nucleotide-free Rab8:Rabin8 crystals were soaked with cryo solution containing 30 % (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6 and 1 mM respective nucleotide GDP/GTP for one hour at 4 C, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.5265.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.587α = 90
b = 164.765β = 90
c = 166.421γ = 90
Symmetry
Space GroupC 2 2 21

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 X10SA0.9840SLSX10SA

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
13.120.19820523201188.313.56

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 REPLACEMENTTHROUGHOUT1YZQ3.120.0819035100398.110.289570.288480.31031RANDOM89.471
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]
2.683.74-6.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.275
r_dihedral_angle_3_deg23.421
r_dihedral_angle_4_deg22.287
r_dihedral_angle_1_deg7.651
r_angle_other_deg4.425
r_angle_refined_deg1.708
r_symmetry_hbond_refined0.531
r_nbd_refined0.27
r_symmetry_vdw_other0.264
r_nbd_other0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.275
r_dihedral_angle_3_deg23.421
r_dihedral_angle_4_deg22.287
r_dihedral_angle_1_deg7.651
r_angle_other_deg4.425
r_angle_refined_deg1.708
r_symmetry_hbond_refined0.531
r_nbd_refined0.27
r_symmetry_vdw_other0.264
r_nbd_other0.24
r_symmetry_vdw_refined0.231
r_nbtor_refined0.201
r_xyhbond_nbd_refined0.182
r_nbtor_other0.117
r_xyhbond_nbd_other0.087
r_chiral_restr0.082
r_bond_refined_d0.017
r_gen_planes_refined0.005
r_gen_planes_other0.005
r_bond_other_d
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4727
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms61

Software

Software
Software NamePurpose
MOSFLMdata reduction
PHASESphasing
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling