5UOJ

THE STRUCTURE OF THE MAP KINASE P38 AT 2.1 ANGSTROMS RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ERK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP289.1518% polyethylene glycol (PEG) 8000, 0.2 M Mg(OAc)2, 0.1 M Hepes, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.9258

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.756α = 90
b = 84.928β = 90
c = 123.911γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate1996-01-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C1.0NSLSX12C

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
12.137.3860.042208.125393
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)
12.12.1665.60.2425.3

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 REPLACEMENTTHROUGHOUT1ERK2.170.0524191129685.920.156740.153730.2142RANDOM33.292
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]
0.24-0.290.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.782
r_dihedral_angle_4_deg18.84
r_dihedral_angle_3_deg13.81
r_long_range_B_refined8.544
r_long_range_B_other8.472
r_dihedral_angle_1_deg6.882
r_scangle_other6.01
r_mcangle_it4.685
r_mcangle_other4.685
r_scbond_it3.808
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.782
r_dihedral_angle_4_deg18.84
r_dihedral_angle_3_deg13.81
r_long_range_B_refined8.544
r_long_range_B_other8.472
r_dihedral_angle_1_deg6.882
r_scangle_other6.01
r_mcangle_it4.685
r_mcangle_other4.685
r_scbond_it3.808
r_scbond_other3.807
r_mcbond_it3.189
r_mcbond_other3.18
r_angle_refined_deg1.879
r_angle_other_deg1.045
r_chiral_restr0.115
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2763
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data scaling