5OQ6

Structure of CHK1 12-pt. mutant complex with aminopyrimido-benzodiazepinone LRRK2 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OOT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52937% PEG 8000, 0.1 M MES buffer pH 6.5, 20% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.3547.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45α = 90
b = 66.16β = 101.84
c = 54.98γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2012-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
11.9144.0498.50.0510.0630.0360.99813.72.924224
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.911.9698.20.5550.6950.4130.7732.6

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 REPLACEMENTTHROUGHOUT5OOT1.953021610116498.480.15970.15780.1918RANDOM40.027
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]
-2.47-1.05-0.793.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.963
r_dihedral_angle_4_deg19.286
r_dihedral_angle_3_deg18.417
r_dihedral_angle_1_deg5.684
r_angle_refined_deg1.949
r_angle_other_deg1.123
r_chiral_restr0.13
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.963
r_dihedral_angle_4_deg19.286
r_dihedral_angle_3_deg18.417
r_dihedral_angle_1_deg5.684
r_angle_refined_deg1.949
r_angle_other_deg1.123
r_chiral_restr0.13
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2071
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms43

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction