4EWQ

Human p38 alpha MAPK in complex with a pyridazine based inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HVCPDB ENTRY 3HVC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52950.1M Ammonium Acetate, 0.1< BisTris (pH 5.5), 17% PEG 10,000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1141.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.257α = 90
b = 74.276β = 90
c = 76.815γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDDIAMOND2011-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
12.1301000.06423.84.9224552245511
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)
12.12.141000.572.74.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3HVC2.129.762245521240114699.950.182140.179640.22919RANDOM35.589
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]
-1.29-1.923.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.438
r_dihedral_angle_4_deg14.455
r_dihedral_angle_3_deg11.501
r_scangle_it4.796
r_scbond_it3.194
r_dihedral_angle_1_deg2.86
r_mcangle_it2.083
r_angle_refined_deg1.439
r_mcbond_it1.213
r_angle_other_deg0.821
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.438
r_dihedral_angle_4_deg14.455
r_dihedral_angle_3_deg11.501
r_scangle_it4.796
r_scbond_it3.194
r_dihedral_angle_1_deg2.86
r_mcangle_it2.083
r_angle_refined_deg1.439
r_mcbond_it1.213
r_angle_other_deg0.821
r_mcbond_other0.343
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2808
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms101

Software

Software
Software NamePurpose
HKL-2000data collection
Cootmodel building
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling