4EPV

Discovery of Small Molecules that Bind to K-Ras and Inhibit Sos-mediated Activation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EPT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP429125% PEG1500, 0.1 M MMT, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9135.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.14α = 90
b = 41.066β = 90
c = 91.955γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352010-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
11.3545.9896.90.09214.24.13331232293-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.3772.40.24.12.2

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4EPT1.3545.983331230436162196.340.165440.163930.19385RANDOM13.884
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]
-0.350.51-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.267
r_dihedral_angle_4_deg19.952
r_dihedral_angle_3_deg11.66
r_dihedral_angle_1_deg5.613
r_scangle_it4.82
r_scbond_it3.119
r_angle_refined_deg2.354
r_mcangle_it2.11
r_mcbond_it1.295
r_chiral_restr0.158
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.267
r_dihedral_angle_4_deg19.952
r_dihedral_angle_3_deg11.66
r_dihedral_angle_1_deg5.613
r_scangle_it4.82
r_scbond_it3.119
r_angle_refined_deg2.354
r_mcangle_it2.11
r_mcbond_it1.295
r_chiral_restr0.158
r_bond_refined_d0.029
r_gen_planes_refined0.014
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1355
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms48

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling