5OPR

Structure of CHK1 10-pt. mutant complex with aminopyridine LRRK2 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

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
2.3146.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.986α = 90
b = 65.826β = 101.82
c = 54.237γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2012-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.7841.32498.40.0590.0720.04110.2329281
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.8493.80.5110.5110.6390.3771.52.5

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 REPLACEMENTTHROUGHOUT5OOP1.952021288111898.750.16570.16360.2061RANDOM41.893
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]
-2.51-0.090.242.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.654
r_dihedral_angle_4_deg21.544
r_dihedral_angle_3_deg18.003
r_dihedral_angle_1_deg6.118
r_angle_refined_deg1.939
r_angle_other_deg1.106
r_chiral_restr0.127
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.654
r_dihedral_angle_4_deg21.544
r_dihedral_angle_3_deg18.003
r_dihedral_angle_1_deg6.118
r_angle_refined_deg1.939
r_angle_other_deg1.106
r_chiral_restr0.127
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2054
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms28

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction