1ZVQ

Structure of the Q61G mutant of Ras in the GDP-bound form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Q21PDB ENTRY 4Q21

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529318% PEG4000, 50 mM Ca Acetate, 10 mM MgCl2, 100 mM Tris-HCl, 250 mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6854.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.992α = 90
b = 92.992β = 90
c = 121.015γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Monochromator2004-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26C1.00NSLSX26C

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
1238.298.80.07824.17.11390613739226.8
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)
122.0791.879.50.4972.63.11257

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4Q21238.2139061304969098.790.1880.1880.1860.229RANDOM30.795
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]
-1.56-0.78-1.562.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.557
r_dihedral_angle_4_deg18.367
r_dihedral_angle_3_deg14.62
r_dihedral_angle_1_deg5.638
r_scangle_it2.758
r_scbond_it1.757
r_angle_refined_deg1.268
r_mcangle_it1.054
r_mcbond_it0.672
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.557
r_dihedral_angle_4_deg18.367
r_dihedral_angle_3_deg14.62
r_dihedral_angle_1_deg5.638
r_scangle_it2.758
r_scbond_it1.757
r_angle_refined_deg1.268
r_mcangle_it1.054
r_mcbond_it0.672
r_nbtor_refined0.306
r_nbd_refined0.205
r_symmetry_vdw_refined0.155
r_xyhbond_nbd_refined0.138
r_symmetry_hbond_refined0.114
r_chiral_restr0.079
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1317
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms30

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing