5OQ5

Structure of CHK1 8-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
2.3948.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.4α = 90
b = 66.57β = 101.58
c = 55.08γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9282DiamondI04-1

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
11.3833.2896.40.0270.0330.0190.998182.763516
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)
11.381.4289.40.7871.0090.6240.6122.1

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 REPLACEMENTTHROUGHOUT5OOT1.42058098301396.640.16950.16870.1852RANDOM32.723
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]
-1.45-0.490.111.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.495
r_dihedral_angle_4_deg21.177
r_dihedral_angle_3_deg15.434
r_dihedral_angle_1_deg5.61
r_angle_refined_deg2.554
r_angle_other_deg1.19
r_chiral_restr0.15
r_bond_refined_d0.029
r_gen_planes_refined0.013
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.495
r_dihedral_angle_4_deg21.177
r_dihedral_angle_3_deg15.434
r_dihedral_angle_1_deg5.61
r_angle_refined_deg2.554
r_angle_other_deg1.19
r_chiral_restr0.15
r_bond_refined_d0.029
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2106
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction