6GJ7

CRYSTAL STRUCTURE OF KRAS G12D (GPPCP) IN COMPLEX WITH 22


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298Molecular Dimensions Morpheus Screen with 30% Precipitant Mix1, 0.1M Morpheus buffer system 2 pH 7.5 and 10% nitrate phosphate sulfate mix
Crystal Properties
Matthews coefficientSolvent content
2.8957.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.79α = 90
b = 116.672β = 90
c = 91.802γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2017-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00003SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.6758.3361000.1860.1869.96.42077216.21
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9251.93288.42.16.2

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 REPLACEMENTTHROUGHOUT4EPV1.674020772102178.30.2270.2260.257RANDOM20.03
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]
-3.6159-6.417310.0332
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion17.78
t_omega_torsion2.8
t_angle_deg1.01
t_bond_d0.008
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion17.78
t_omega_torsion2.8
t_angle_deg1.01
t_bond_d0.008
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1325
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms72

Software

Software
Software NamePurpose
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
BUSTERrefinement
PHASERphasing