2FN4

The crystal structure of human Ras-related protein, RRAS, in the GDP-bound state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ERY2ERY.pdb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52931.6M Na/KPO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0740.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.152α = 90
b = 43.152β = 90
c = 155.499γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00008SLSX10SA

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
11.655095.76.120362
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.711005.1

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2ERY.pdb1.6537.41918019180103995.690.21650.21650.214680.2506RANDOM30.889
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]
0.330.160.33-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.789
r_dihedral_angle_4_deg15.926
r_dihedral_angle_3_deg13.135
r_dihedral_angle_1_deg6.168
r_scangle_it2.585
r_scbond_it1.741
r_angle_refined_deg1.39
r_mcangle_it1.077
r_angle_other_deg0.936
r_mcbond_it0.776
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.789
r_dihedral_angle_4_deg15.926
r_dihedral_angle_3_deg13.135
r_dihedral_angle_1_deg6.168
r_scangle_it2.585
r_scbond_it1.741
r_angle_refined_deg1.39
r_mcangle_it1.077
r_angle_other_deg0.936
r_mcbond_it0.776
r_symmetry_vdw_other0.224
r_nbd_refined0.211
r_nbd_other0.205
r_mcbond_other0.198
r_symmetry_vdw_refined0.184
r_symmetry_hbond_refined0.183
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.163
r_metal_ion_refined0.16
r_chiral_restr0.088
r_nbtor_other0.083
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1344
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing