3ZS5

Structural basis for kinase selectivity of three clinical p38alpha inhibitors


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5HANGING DROP, ROOM TEMP, 20 MM HEPES PH7.1, 50 MM NACL, 10 MM DTT, 5% GLYCEROL, 0.1 G/L METHIONINE, 28% PEG 4K,0.1 M MES PH=6.5, 50 MM N-OCTYL-BETAGLUCOSIDE. CRYOPROTECTANT 28% PEG 4K, 0.1M MES PH5.9, 50 MM N-OCTYL-BETAGLUCOSIDE, 20% ETHYLENE GLYCOL.
Crystal Properties
Matthews coefficientSolvent content
2.3347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.492α = 90
b = 70.036β = 90
c = 75.01γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.640.793.80.0886.944440
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)
11.61.6975.30.882.25.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.651.1642175223293.340.185860.184330.21527RANDOM20.088
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]
0.18-0.14-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.472
r_dihedral_angle_4_deg15.275
r_dihedral_angle_3_deg12.879
r_dihedral_angle_1_deg6.366
r_scangle_it2.776
r_mcangle_it2.367
r_scbond_it1.768
r_mcbond_it1.458
r_angle_refined_deg1.271
r_angle_other_deg0.844
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.472
r_dihedral_angle_4_deg15.275
r_dihedral_angle_3_deg12.879
r_dihedral_angle_1_deg6.366
r_scangle_it2.776
r_mcangle_it2.367
r_scbond_it1.768
r_mcbond_it1.458
r_angle_refined_deg1.271
r_angle_other_deg0.844
r_mcbond_other0.363
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2740
Nucleic Acid Atoms
Solvent Atoms291
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing