5OCT

Discovery of small molecules binding to KRAS via high affinity antibody fragment competition method.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GFT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2918-15% w/v PEG 3350 and 0.2 M lithium citrate
Crystal Properties
Matthews coefficientSolvent content
2.4750.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.49α = 90
b = 118.45β = 90
c = 155.36γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim 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
12.0741.721000.20.0670.99812.212.972162

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 REPLACEMENTTHROUGHOUT3GFT2.0741.7268511357399.840.189360.187870.21843RANDOM42.632
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]
-1.051.99-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.602
r_dihedral_angle_4_deg17.237
r_dihedral_angle_3_deg14.777
r_long_range_B_refined10.931
r_long_range_B_other10.931
r_scangle_other8.695
r_dihedral_angle_1_deg6.109
r_scbond_it5.704
r_scbond_other5.704
r_mcangle_it5.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.602
r_dihedral_angle_4_deg17.237
r_dihedral_angle_3_deg14.777
r_long_range_B_refined10.931
r_long_range_B_other10.931
r_scangle_other8.695
r_dihedral_angle_1_deg6.109
r_scbond_it5.704
r_scbond_other5.704
r_mcangle_it5.52
r_mcangle_other5.52
r_mcbond_it3.86
r_mcbond_other3.859
r_angle_refined_deg1.802
r_angle_other_deg1.031
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms7984
Nucleic Acid Atoms
Solvent Atoms370
Heterogen Atoms326

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
Cootmodel building