5OQ8

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OP2 

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
2.3547.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.88α = 90
b = 65.86β = 99.58
c = 55.06γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2012-08-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
11.9744.2598.40.0740.0910.0530.99610.92.822077
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)
11.972.0299.30.7860.9780.5730.3792.7

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 REPLACEMENTTHROUGHOUT5OP224020025106698.120.16690.1650.1998RANDOM42.26
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]
-1.320.44-0.861.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.173
r_dihedral_angle_4_deg23.205
r_dihedral_angle_3_deg19.552
r_dihedral_angle_1_deg5.763
r_angle_refined_deg1.898
r_angle_other_deg1.136
r_chiral_restr0.135
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.173
r_dihedral_angle_4_deg23.205
r_dihedral_angle_3_deg19.552
r_dihedral_angle_1_deg5.763
r_angle_refined_deg1.898
r_angle_other_deg1.136
r_chiral_restr0.135
r_bond_refined_d0.018
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 Atoms2096
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms30

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction