X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YZQPDB ENTRY 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 hours at 278 K, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.5965.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.337α = 90
b = 165.561β = 90
c = 167.263γ = 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 X10SA1.0000SLSX10SA

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
13.22099.419050189329.99.54

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 1YZQ3.219.991790595499.530.279180.277610.30877RANDOM92.122
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]
4.282.11-6.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.704
r_dihedral_angle_3_deg23.436
r_dihedral_angle_4_deg21.853
r_dihedral_angle_1_deg7.52
r_angle_other_deg4.439
r_scangle_it3.415
r_scbond_it2.118
r_mcangle_it1.995
r_angle_refined_deg1.639
r_mcbond_it1.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.704
r_dihedral_angle_3_deg23.436
r_dihedral_angle_4_deg21.853
r_dihedral_angle_1_deg7.52
r_angle_other_deg4.439
r_scangle_it3.415
r_scbond_it2.118
r_mcangle_it1.995
r_angle_refined_deg1.639
r_mcbond_it1.095
r_mcbond_other1.082
r_nbd_refined0.268
r_symmetry_vdw_other0.25
r_nbd_other0.24
r_nbtor_refined0.203
r_symmetry_vdw_refined0.192
r_xyhbond_nbd_refined0.161
r_nbtor_other0.114
r_xyhbond_nbd_other0.106
r_chiral_restr0.076
r_symmetry_hbond_refined0.056
r_bond_refined_d0.016
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_mcangle_other
r_scbond_other
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 Atoms4735
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms64

Software

Software
Software NamePurpose
MOSFLMdata reduction
PHASESphasing
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling