3FSF

P38 kinase crystal structure in complex with 3-(2,6-Dichloro-phenyl)-7-[4-(2-diethylamino-ethoxy)-phenylamino]-1-methyl-3,4-dihydro-1H-pyrimido[4,5-d]pyrimidin-2-one


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.629050 mM Hepes pH 7.6, 50 mM CaCl2, 17% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.8356.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.202α = 90
b = 86.402β = 90
c = 124.158γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.1ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.11097.50.0894.82819022
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.17850.217.42.4

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 1P382.19.9627856276396.40.2250.259RANDOM33.1
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]
-5.34-1.216.55
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.4
c_scangle_it1.8
c_mcangle_it1.56
c_angle_deg1.4
c_scbond_it1.15
c_mcbond_it0.9
c_improper_angle_d0.87
c_bond_d0.012
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.4
c_scangle_it1.8
c_mcangle_it1.56
c_angle_deg1.4
c_scbond_it1.15
c_mcbond_it0.9
c_improper_angle_d0.87
c_bond_d0.012
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 Atoms2751
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms34

Software

Software
Software NamePurpose
ADSCdata collection
CNSrefinement
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing