4HDQ

Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and the Heart of Glass (HEG1) cytoplasmic tail


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.527815% PEG2000 MME, 100 mM Tris, 100 mM potassium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.1743.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.31α = 90
b = 77.41β = 95.56
c = 58.57γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2010-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.979DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.953099.10.06620.993.33696336963
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0796.80.3473.92.916656

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-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4HDO1.9529.1535112184899.210.203420.203420.200440.26278RANDOM32.365
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]
-1.40.971.270.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.752
r_dihedral_angle_4_deg20.053
r_dihedral_angle_3_deg17.137
r_dihedral_angle_1_deg7.455
r_angle_refined_deg1.932
r_angle_other_deg1.038
r_chiral_restr0.118
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.752
r_dihedral_angle_4_deg20.053
r_dihedral_angle_3_deg17.137
r_dihedral_angle_1_deg7.455
r_angle_refined_deg1.932
r_angle_other_deg1.038
r_chiral_restr0.118
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3877
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms39

Software

Software
Software NamePurpose
dlsdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling