9GTK | pdb_00009gtk

KRAS in complex with DARPin 784_F5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YDW 
experimental modelPDB 5F2E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.15Crystals grew within 25 days in 0.2 M potassium sodium tartrate, 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.7455.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.32α = 90
b = 152.83β = 90
c = 149.15γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2016-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12481000.0820.0880.99914.287.2173930
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.052.2422.4130.361

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT247.2886336454499.950.172490.171010.18230.200630.2087RANDOM63.756
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]
0.020.22-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.028
r_dihedral_angle_2_deg10.52
r_long_range_B_refined9.352
r_long_range_B_other9.314
r_dihedral_angle_1_deg6.086
r_scangle_other5.604
r_scbond_it4.102
r_scbond_other4.095
r_mcangle_it3.679
r_mcangle_other3.679
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.028
r_dihedral_angle_2_deg10.52
r_long_range_B_refined9.352
r_long_range_B_other9.314
r_dihedral_angle_1_deg6.086
r_scangle_other5.604
r_scbond_it4.102
r_scbond_other4.095
r_mcangle_it3.679
r_mcangle_other3.679
r_mcbond_it2.539
r_mcbond_other2.539
r_angle_refined_deg1.704
r_angle_other_deg0.595
r_chiral_restr0.085
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_4_deg
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 Atoms7825
Nucleic Acid Atoms
Solvent Atoms564
Heterogen Atoms288

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing