2W83

Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J5XPDB ENTRY 2J5X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
12.0 M AMONIUM SULFATE, 0.1 M HEPES PH 7.5, 0.2 M NACL, 2 MM MGCL2, 6 % MPD
Crystal Properties
Matthews coefficientSolvent content
2.9958.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.27α = 90
b = 137.27β = 90
c = 165.03γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287IMAGE PLATEMAR555 FLAT PANEL2008-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.933599.90.06812.8621652
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.932.0398.20.42.111.8

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 2J5X1.93118.6862165698799.90.2170.2140.238RANDOM30.43
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]
1.030.521.03-1.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.731
r_dihedral_angle_3_deg15.539
r_dihedral_angle_4_deg15.156
r_dihedral_angle_1_deg5.367
r_scangle_it2.462
r_scbond_it1.541
r_angle_refined_deg1.17
r_mcangle_it1.104
r_mcbond_it0.686
r_symmetry_hbond_refined0.335
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.731
r_dihedral_angle_3_deg15.539
r_dihedral_angle_4_deg15.156
r_dihedral_angle_1_deg5.367
r_scangle_it2.462
r_scbond_it1.541
r_angle_refined_deg1.17
r_mcangle_it1.104
r_mcbond_it0.686
r_symmetry_hbond_refined0.335
r_nbtor_refined0.299
r_symmetry_vdw_refined0.258
r_nbd_refined0.19
r_xyhbond_nbd_refined0.103
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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 Atoms4931
Nucleic Acid Atoms
Solvent Atoms274
Heterogen Atoms141

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing