2P33

Synthesis and SAR of Aminopyrimidines as Novel c-Jun N-Terminal Kinase (JNK) Inhibitors


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JNKPDB entry 1jnk

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.3647.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.82α = 90
b = 71.52β = 90
c = 107.36γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic2004-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.42095.30.06823.26.5153403.533.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.4489.80.3253.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1jnk2.419.8415302155094.60.2530.304RANDOM49
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]
31.61-13.87-17.74
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.6
c_scangle_it2.8
c_mcangle_it2.43
c_scbond_it1.88
c_mcbond_it1.4
c_angle_deg1.2
c_improper_angle_d0.72
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.6
c_scangle_it2.8
c_mcangle_it2.43
c_scbond_it1.88
c_mcbond_it1.4
c_angle_deg1.2
c_improper_angle_d0.72
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2703
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms28

Software

Software
Software NamePurpose
CNXrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNXphasing