4G3X

Crystal Structure of Q61L H-Ras-GppNHp bound to the RBD of Raf Kinase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K8YPDB 3K8Y for Chain A and PDB 1GUA for Chain B
experimental modelPDB 1GUAPDB 3K8Y for Chain A and PDB 1GUA for Chain B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.8291Protein solution: 10 - 18 mg/mL, 50 mM HEPES, pH 7.2, 50 mM NaCl, 10mM MgCl2 5% Glycerol, 1mM DTE, 10 M ZnCl2 Reservoir solution:200mM calcium acetate, 100mM sodium cacodylate pH 6.5, 18% PEG 8000. Drop: 3uL protein, 3uL reservoir , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
4.0669.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.4α = 90
b = 91.4β = 90
c = 93.11γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDcrystal2011-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.2532.60.184.66462646233

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB 3K8Y for Chain A and PDB 1GUA for Chain B3.2532.6633966885.60.27540.25050.271
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]
0.06050.0605-0.1211
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.773
f_angle_d0.597
f_chiral_restr0.041
f_bond_d0.009
f_plane_restr0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1860
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms33

Software

Software
Software NamePurpose
MAR345data collection
SERGUIdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing