4F38

Crystal structure of geranylgeranylated RhoA in complex with RhoGDI in its active GPPNHP-bound form


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429320% (w/v) PEG 3350, 0.2M MgCl2, 0.1M Hepes-NaOH, 25mM Hepes-NaOH pH 7.2, 40mM NaCl, 3mM MgCl2, 10M GMPPNP, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4750.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46α = 90
b = 71.576β = 90
c = 136.03γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102011-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.868.01970.0690.0712.332.721383207416.912.3341.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.998.10.2650.2793.62.72156

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1DOA2.868.013.63.6213832074154498.860.2060.205790.2020.28133RANDOM37.387
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]
2.09-1.86-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.079
r_dihedral_angle_3_deg23.045
r_dihedral_angle_4_deg20.555
r_dihedral_angle_1_deg7.704
r_scangle_it3.696
r_scbond_it2.095
r_angle_refined_deg1.743
r_mcangle_it1.415
r_mcbond_it0.716
r_chiral_restr0.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.079
r_dihedral_angle_3_deg23.045
r_dihedral_angle_4_deg20.555
r_dihedral_angle_1_deg7.704
r_scangle_it3.696
r_scbond_it2.095
r_angle_refined_deg1.743
r_mcangle_it1.415
r_mcbond_it0.716
r_chiral_restr0.117
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2992
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms54

Software

Software
Software NamePurpose
ADSCdata collection
PHASESphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling