1R8S

ARF1[DELTA1-17]-GDP IN COMPLEX WITH A SEC7 DOMAIN CARRYING THE MUTATION OF THE CATALYTIC GLUTAMATE TO LYSINE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R8RPDB ENTRY 1R8R and crystal structure of the Arf1[D1-17]/Gea2-Sec7 complex (Goldberg, J., (1998) Cell 95(2):237-48)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62891.88M Ammonium Sulfate, 100mM MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.5651.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.018α = 90
b = 104.018β = 90
c = 69.277γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-30.931ESRFID14-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.46300.05926.6167505118.35
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.461.47970.4625.912.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1R8R and crystal structure of the Arf1[D1-17]/Gea2-Sec7 complex (Goldberg, J., (1998) Cell 95(2):237-48)1.4628.877505171299374499.910.159410.158850.1698RANDOM12.525
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]
-0.05-0.02-0.050.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.153
r_scangle_it4.08
r_scbond_it2.529
r_mcangle_it1.68
r_angle_refined_deg1.421
r_mcbond_it0.881
r_angle_other_deg0.87
r_symmetry_vdw_refined0.56
r_symmetry_vdw_other0.31
r_nbd_other0.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.153
r_scangle_it4.08
r_scbond_it2.529
r_mcangle_it1.68
r_angle_refined_deg1.421
r_mcbond_it0.881
r_angle_other_deg0.87
r_symmetry_vdw_refined0.56
r_symmetry_vdw_other0.31
r_nbd_other0.246
r_symmetry_hbond_refined0.222
r_nbd_refined0.218
r_xyhbond_nbd_refined0.143
r_chiral_restr0.086
r_nbtor_other0.085
r_gen_planes_other0.022
r_bond_other_d0.018
r_bond_refined_d0.015
r_gen_planes_refined0.013
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2806
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
CCP4phasing