5OP7

Structure of CHK1 10-pt. mutant complex with pyrrolopyrimidine 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
2.3146.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.07α = 90
b = 65.62β = 101.99
c = 54.37γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.97857SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.752097.80.040.0490.99915.692.97930900-336.053
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.85950.5620.6860.772.232.921

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 REPLACEMENTTHROUGHOUT5OOP1.82026870146098.320.16830.16580.2154RANDOM36.629
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]
-1.8-0.140.131.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.953
r_dihedral_angle_4_deg18.464
r_dihedral_angle_3_deg15.835
r_dihedral_angle_1_deg5.915
r_angle_refined_deg1.95
r_angle_other_deg1.065
r_chiral_restr0.129
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.953
r_dihedral_angle_4_deg18.464
r_dihedral_angle_3_deg15.835
r_dihedral_angle_1_deg5.915
r_angle_refined_deg1.95
r_angle_other_deg1.065
r_chiral_restr0.129
r_bond_refined_d0.019
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 Atoms2090
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms31

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction