3IW8

Structure of Inactive Human p38 MAP Kinase in Complex with a Thiazole-Urea


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZYJPDB ENTRY 1zyj

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293100mM MES, 20-30% PEG 4000, 50mM n-BOG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1643.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.37α = 90
b = 69.84β = 90
c = 74.7γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMARRESEARCHDynamically bendable mirror2008-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.976416SLSX10SA

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
124098.30.04422.414.112480324384-336.194
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)
22.197.80.3814.54.183310

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 1zyj24024803243818531000.220.2170.298RANDOM31.905
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]
0.81-0.880.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.306
r_dihedral_angle_4_deg16.598
r_dihedral_angle_3_deg14.974
r_dihedral_angle_1_deg5.446
r_scangle_it3.618
r_scbond_it2.332
r_mcangle_it1.685
r_angle_refined_deg1.484
r_mcbond_it1.018
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.306
r_dihedral_angle_4_deg16.598
r_dihedral_angle_3_deg14.974
r_dihedral_angle_1_deg5.446
r_scangle_it3.618
r_scbond_it2.332
r_mcangle_it1.685
r_angle_refined_deg1.484
r_mcbond_it1.018
r_nbtor_refined0.309
r_symmetry_hbond_refined0.237
r_nbd_refined0.214
r_xyhbond_nbd_refined0.183
r_symmetry_vdw_refined0.151
r_chiral_restr0.105
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2694
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms48

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction