6EPO

RAS GUANINE EXCHANGE FACTOR SOS1 (REM-CDC25) IN COMPLEX WITH KRAS(G12C) AND FRAGMENT SCREENING HIT F3


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277Drops made from KRAS SOS1 complex (14.4 mg/ml in 5 mM Tris pH 7.5, 100mM NaCl) and reservoir solution (2.9 to 3.4 M sodium formate, 100 mM MES pH 6.5). Fragment soaked at 25 mM for two days using a 500 mM fragment stock solution in DMSO. Cryo buffer 0.1 M MES pH 6.5, 3.5 M sodium formate, 20 glycerol, 25 mM fragment
Crystal Properties
Matthews coefficientSolvent content
3.6866.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.118α = 90
b = 150.118β = 90
c = 200.087γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID090.97718ESRFID09

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)CC (Half)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
12.448.5499.90.1150.99813.910.546950454.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5499.80.9240.7662.310.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1bkd2.448.5443123173699.950.187360.186290.21363RANDOM58.224
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]
-0.45-0.450.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.724
r_dihedral_angle_3_deg16.821
r_dihedral_angle_4_deg16.285
r_long_range_B_other9.48
r_long_range_B_refined9.479
r_scangle_other7.126
r_dihedral_angle_1_deg5.756
r_mcangle_it5.591
r_mcangle_other5.591
r_scbond_it4.525
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.724
r_dihedral_angle_3_deg16.821
r_dihedral_angle_4_deg16.285
r_long_range_B_other9.48
r_long_range_B_refined9.479
r_scangle_other7.126
r_dihedral_angle_1_deg5.756
r_mcangle_it5.591
r_mcangle_other5.591
r_scbond_it4.525
r_scbond_other4.524
r_mcbond_it3.563
r_mcbond_other3.561
r_angle_refined_deg1.348
r_angle_other_deg0.974
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5156
Nucleic Acid Atoms
Solvent Atoms302
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing