3QUD

Human p38 MAP Kinase in Complex with 2-amino-phenylamino-benzophenone


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293100 mM MES, 20-30% PEG 4000, 50mM n-BOG, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3647.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.779α = 90
b = 73.368β = 90
c = 79.591γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90PIXELPSI PILATUS 6MDynamic bendable mirror2011-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000000SLSX10SA

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
124598.80.05719.14.132706826734-335.687
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.199.40.4340.4953.74.33618

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 REPLACEMENTTHROUGHOUT1ZYJ241.9626733267339361000.23350.23180.278RANDOM28.8361
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]
-0.1-11.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.779
r_dihedral_angle_4_deg20.981
r_dihedral_angle_3_deg16.697
r_dihedral_angle_1_deg5.622
r_scangle_it3.276
r_scbond_it1.984
r_mcangle_it1.427
r_angle_refined_deg1.294
r_mcbond_it0.768
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.779
r_dihedral_angle_4_deg20.981
r_dihedral_angle_3_deg16.697
r_dihedral_angle_1_deg5.622
r_scangle_it3.276
r_scbond_it1.984
r_mcangle_it1.427
r_angle_refined_deg1.294
r_mcbond_it0.768
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2772
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms62

Software

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