6QYX

p38(alpha) MAP kinase with the activation loop of ERK2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherp38 wild type

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1 M HEPES pH 7.5, 0.2 M KF, 13%-17% (w/v) PEG 3350, 25 mM beta-D-octyl glucoside (bOG)
Crystal Properties
Matthews coefficientSolvent content
2.346.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.86α = 90
b = 74.5β = 90
c = 75.28γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2015-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873ESRFID23-2

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
11.6652.9599.10.0689.84.246102
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)
11.661.720.862

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 REPLACEMENTTHROUGHOUTp38 wild type1.6652.9543882216899.140.187740.184850.24233RANDOM37.548
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]
-2.44.29-1.9
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.502
r_dihedral_angle_2_deg33.25
r_sphericity_bonded27.03
r_dihedral_angle_4_deg21.886
r_dihedral_angle_3_deg16.994
r_long_range_B_refined10.335
r_long_range_B_other10.326
r_scangle_other9.624
r_mcangle_it8.337
r_mcangle_other8.335
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.502
r_dihedral_angle_2_deg33.25
r_sphericity_bonded27.03
r_dihedral_angle_4_deg21.886
r_dihedral_angle_3_deg16.994
r_long_range_B_refined10.335
r_long_range_B_other10.326
r_scangle_other9.624
r_mcangle_it8.337
r_mcangle_other8.335
r_scbond_it7.851
r_scbond_other7.85
r_dihedral_angle_1_deg6.785
r_mcbond_it6.736
r_mcbond_other6.726
r_rigid_bond_restr3.064
r_angle_refined_deg1.804
r_angle_other_deg0.908
r_chiral_restr0.114
r_bond_refined_d0.017
r_gen_planes_refined0.007
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2731
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing