2ERY | pdb_00002ery

The crystal structure of the Ras related protein RRas2 (RRAS2) in the GDP bound state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X1RPDB ID 1X1R.PDB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.52778 % PEG3350, 0.005 M MgCl2, 0.005 M CoCl2, 0.1 M Bis Tris, 0.1 M Mg(Formate)2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 5.50
Crystal Properties
Matthews coefficientSolvent content
2.346.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.191α = 90
b = 72.115β = 90
c = 82.073γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-10-01MSINGLE 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
11.75098.95.840966
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7692.73.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ID 1X1R.PDB1.7503884838848206298.90.1980.1960.210.2330.19RANDOM18.16
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]
-23.24-1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.775
r_dihedral_angle_3_deg13.636
r_dihedral_angle_4_deg12.328
r_dihedral_angle_1_deg8.911
r_scangle_it2.292
r_angle_other_deg1.575
r_scbond_it1.575
r_angle_refined_deg1.352
r_mcangle_it0.997
r_mcbond_it0.693
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.775
r_dihedral_angle_3_deg13.636
r_dihedral_angle_4_deg12.328
r_dihedral_angle_1_deg8.911
r_scangle_it2.292
r_angle_other_deg1.575
r_scbond_it1.575
r_angle_refined_deg1.352
r_mcangle_it0.997
r_mcbond_it0.693
r_symmetry_vdw_other0.209
r_nbd_refined0.193
r_nbd_other0.179
r_symmetry_vdw_refined0.178
r_nbtor_refined0.176
r_mcbond_other0.162
r_chiral_restr0.15
r_xyhbond_nbd_refined0.133
r_symmetry_hbond_refined0.123
r_nbtor_other0.083
r_metal_ion_refined0.029
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2688
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms58

Software

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