6FA2

Antibody derived (Abd-5) small molecule binding to KRAS.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52778-15% w/v Polyethylene glycol 3350 and 0.2M lithium citrate
Crystal Properties
Matthews coefficientSolvent content
2.4649.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.23α = 90
b = 117.215β = 90
c = 156.446γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.693.811000.0580.0670.0330.99519.17.436640
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.720.880.748

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.693.8134830172399.910.204550.20320.23301RANDOM63.248
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]
-3.249.14-5.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.094
r_dihedral_angle_3_deg15.904
r_dihedral_angle_4_deg14.841
r_long_range_B_refined12.233
r_long_range_B_other12.232
r_scangle_other9.577
r_mcangle_it7.504
r_mcangle_other7.504
r_scbond_it6.084
r_scbond_other6.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.094
r_dihedral_angle_3_deg15.904
r_dihedral_angle_4_deg14.841
r_long_range_B_refined12.233
r_long_range_B_other12.232
r_scangle_other9.577
r_mcangle_it7.504
r_mcangle_other7.504
r_scbond_it6.084
r_scbond_other6.083
r_dihedral_angle_1_deg5.504
r_mcbond_it4.959
r_mcbond_other4.958
r_angle_refined_deg1.702
r_angle_other_deg0.947
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms7700
Nucleic Acid Atoms
Solvent Atoms28
Heterogen Atoms402

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
PHASERphasing