5TAR

Crystal structure of farnesylated and methylated kras4b in complex with PDE-delta (crystal form II - with ordered hypervariable region)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OBE4OBE, 3T5G
experimental modelPDB 3T5G4OBE, 3T5G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M HEPES:NaOH pH 7.5 and 2 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.2745.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.14α = 90
b = 70.495β = 90
c = 84.684γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-08-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.979200APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.950.0199.80.0620.99919.567.227609-337.255
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.96990.820.7973.37.2

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 REPLACEMENTTHROUGHOUT4OBE, 3T5G1.950.0126207181999.770.225960.223260.26575RANDOM37.483
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]
-0.5-1.261.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.011
r_dihedral_angle_3_deg14.394
r_dihedral_angle_4_deg14.298
r_dihedral_angle_1_deg5.654
r_long_range_B_refined4.809
r_long_range_B_other4.809
r_scangle_other3.318
r_mcangle_it2.666
r_mcangle_other2.666
r_scbond_it1.981
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.011
r_dihedral_angle_3_deg14.394
r_dihedral_angle_4_deg14.298
r_dihedral_angle_1_deg5.654
r_long_range_B_refined4.809
r_long_range_B_other4.809
r_scangle_other3.318
r_mcangle_it2.666
r_mcangle_other2.666
r_scbond_it1.981
r_scbond_other1.981
r_mcbond_it1.656
r_mcbond_other1.653
r_angle_refined_deg1.302
r_angle_other_deg0.854
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms2672
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building