6UZK

Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi6


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320-25% PEG 3,350, 100 mM Tris, pH 8.5, 100 mM KCl
Crystal Properties
Matthews coefficientSolvent content
2.3748.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.204α = 90
b = 77.089β = 91.558
c = 58.41γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2019-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.999995ALS5.0.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9250940.99116.33336147
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.921.950.486

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4hdo1.92436.51436123177293.7120.2230.22010.286148.081
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]
-0.8342.847-1.4632.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.315
r_dihedral_angle_4_deg18.472
r_dihedral_angle_3_deg18.01
r_dihedral_angle_1_deg7.056
r_lrange_it6.197
r_mcangle_it3.309
r_scangle_it2.768
r_mcbond_it1.777
r_scbond_it1.539
r_angle_refined_deg1.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.315
r_dihedral_angle_4_deg18.472
r_dihedral_angle_3_deg18.01
r_dihedral_angle_1_deg7.056
r_lrange_it6.197
r_mcangle_it3.309
r_scangle_it2.768
r_mcbond_it1.777
r_scbond_it1.539
r_angle_refined_deg1.069
r_nbtor_refined0.314
r_nbd_refined0.216
r_symmetry_nbd_refined0.205
r_symmetry_xyhbond_nbd_refined0.183
r_xyhbond_nbd_refined0.128
r_metal_ion_refined0.096
r_chiral_restr0.084
r_gen_planes_refined0.004
r_bond_refined_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3809
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing