6EPL

Ras guanine exchange factor SOS1 (Rem-cdc25) in complex with KRAS(G12C)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5277Drops made from KRAS SOS1 complex (11.3 mg/ml in 5 mM Tris pH 7.5, 100 mM NaCl) and reservoir solution (3.65 M sodium Formate). No cryo protectant added.
Crystal Properties
Matthews coefficientSolvent content
3.6966.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.522α = 90
b = 149.522β = 90
c = 202.101γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2014-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
12.5548.4990.1550.1640.997139.53737344
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.798.30.8850.9420.5922.28.6

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1BKD2.5548.39355031869990.191920.190240.2238RANDOM49.401
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]
-0.41-0.410.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.632
r_dihedral_angle_4_deg16.003
r_dihedral_angle_3_deg15.528
r_long_range_B_other6.504
r_long_range_B_refined6.503
r_dihedral_angle_1_deg5.273
r_scangle_other4.189
r_mcangle_it3.897
r_mcangle_other3.897
r_scbond_it2.396
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.632
r_dihedral_angle_4_deg16.003
r_dihedral_angle_3_deg15.528
r_long_range_B_other6.504
r_long_range_B_refined6.503
r_dihedral_angle_1_deg5.273
r_scangle_other4.189
r_mcangle_it3.897
r_mcangle_other3.897
r_scbond_it2.396
r_scbond_other2.39
r_mcbond_it2.243
r_mcbond_other2.243
r_angle_refined_deg1.141
r_angle_other_deg0.903
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
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 Atoms5194
Nucleic Acid Atoms
Solvent Atoms265
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing