X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.8293Rab8a6-176:GppNHp (15 mg/ml; buffer: 25 mM HEPES, 40 mM NaCl, 1 mM MgCl2, 10 M GppNHp and 5 mM -mercaptoethanol) crystals were produced in 15% (w/v) PEG8000, 7.5 %(v/v) MPD, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.381α = 90
b = 96.676β = 90
c = 105.09γ = 90
Symmetry
Space GroupP 21 21 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 X10SASLSX10SA

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
11.5519.999.213260521.62

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 REPLACEMENTTHROUGHOUT1YZQ1.5519.89125855668899.20.1460.1440.183RANDOM17.43
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]
0.74-0.73-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.27
r_dihedral_angle_4_deg18.573
r_dihedral_angle_3_deg15.317
r_dihedral_angle_1_deg6.099
r_scangle_it4.736
r_angle_other_deg4.147
r_scbond_it3.178
r_mcangle_it2.477
r_mcbond_other2.077
r_mcbond_it1.482
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.27
r_dihedral_angle_4_deg18.573
r_dihedral_angle_3_deg15.317
r_dihedral_angle_1_deg6.099
r_scangle_it4.736
r_angle_other_deg4.147
r_scbond_it3.178
r_mcangle_it2.477
r_mcbond_other2.077
r_mcbond_it1.482
r_angle_refined_deg1.479
r_chiral_restr0.334
r_symmetry_vdw_other0.299
r_symmetry_vdw_refined0.255
r_nbd_other0.249
r_nbd_refined0.233
r_symmetry_hbond_refined0.201
r_xyhbond_nbd_refined0.19
r_nbtor_refined0.182
r_nbtor_other0.11
r_metal_ion_refined0.024
r_bond_refined_d0.013
r_gen_planes_other0.007
r_gen_planes_refined0.005
r_bond_other_d
r_xyhbond_nbd_other
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 Atoms6913
Nucleic Acid Atoms
Solvent Atoms1049
Heterogen Atoms173

Software

Software
Software NamePurpose
MOSFLMdata reduction
PHASESphasing
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling