9MHB

Crystal Structure of Human P38 alpha MAPK In Complex with MW01-14-064SRM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4F9Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5292Protein: 20.0 mg/ml, 0.15M Sodium chloride, 0.02M Tris-HCl (pH 8.3), 1mM TCEP; Screen: 0.15M Ammomium acetate, 0.1M Bis-Tris (pH 5.5), 16% (w/v) PEG1000; Soak: 3 hrs, 5mM ligand in screen solution; Cryo: 10% Glycerol in screen solution.
Crystal Properties
Matthews coefficientSolvent content
2.448.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.446α = 90
b = 74.862β = 90
c = 78.065γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim 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
11.65301000.0440.0440.0480.0180.99744.97.447571-326
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.681000.9690.9690.3810.7462.37.4

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 REPLACEMENTTHROUGHOUT1.6528.345229227399.920.173930.172540.20174RANDOM31.536
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]
0.2-0.520.33
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined8.093
r_long_range_B_other8.009
r_dihedral_angle_3_deg7.391
r_scangle_other4.806
r_dihedral_angle_2_deg4.462
r_mcangle_it3.177
r_mcangle_other3.176
r_scbond_it3.131
r_scbond_other3.13
r_dihedral_angle_1_deg3.033
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined8.093
r_long_range_B_other8.009
r_dihedral_angle_3_deg7.391
r_scangle_other4.806
r_dihedral_angle_2_deg4.462
r_mcangle_it3.177
r_mcangle_other3.176
r_scbond_it3.131
r_scbond_other3.13
r_dihedral_angle_1_deg3.033
r_mcbond_it2.085
r_mcbond_other2.051
r_angle_refined_deg1.524
r_angle_other_deg0.519
r_chiral_restr0.08
r_gen_planes_refined0.017
r_gen_planes_other0.013
r_bond_refined_d0.005
r_bond_other_d0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2724
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing