2NPQ

A Novel Lipid Binding Site in the p38 alpha MAP Kinase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.2527715% PEG 3350, 0.2M KF, 0.1M Hepes pH 7.25, 25mM BOG, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2545.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.607α = 90
b = 74.212β = 90
c = 74.571γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.939ESRFID14-4

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
11.833.150.06334.63750036965
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)
1.81.830.6011.6

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 REPLACEMENTTHROUGHOUT2FSO1.832.7633741178898.790.205410.203320.24473RANDOM30
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]
-0.010.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.254
r_scangle_it4.344
r_scbond_it2.646
r_mcangle_it1.967
r_angle_refined_deg1.589
r_mcbond_it1.086
r_angle_other_deg0.881
r_symmetry_vdw_other0.265
r_nbd_other0.234
r_nbd_refined0.226
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.254
r_scangle_it4.344
r_scbond_it2.646
r_mcangle_it1.967
r_angle_refined_deg1.589
r_mcbond_it1.086
r_angle_other_deg0.881
r_symmetry_vdw_other0.265
r_nbd_other0.234
r_nbd_refined0.226
r_xyhbond_nbd_refined0.172
r_symmetry_hbond_refined0.163
r_symmetry_vdw_refined0.155
r_chiral_restr0.115
r_nbtor_other0.087
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_gen_planes_other0.005
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2643
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling