5OPV

Structure of CHK1 10-pt. mutant complex with pyrrolopyridine 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
2.5451.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.13α = 90
b = 66.44β = 93.81
c = 57.99γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2012-10-29MSINGLE 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
11.866.44990.1220.1490.0850.9929.2331438
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)
11.81.8599.31.5641.9031.0710.1023.1

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 REPLACEMENTTHROUGHOUT5OOP1.92025351134198.630.1660.1640.2045RANDOM33.823
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]
-1.84-0.53-0.442.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.807
r_dihedral_angle_4_deg18.193
r_dihedral_angle_3_deg16.817
r_dihedral_angle_1_deg5.632
r_angle_refined_deg1.994
r_angle_other_deg1.137
r_chiral_restr0.149
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.807
r_dihedral_angle_4_deg18.193
r_dihedral_angle_3_deg16.817
r_dihedral_angle_1_deg5.632
r_angle_refined_deg1.994
r_angle_other_deg1.137
r_chiral_restr0.149
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2082
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms25

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction