3OC1

Conformational plasticity of p38 MAP kinase DFG motif mutants in response to inhibitor binding


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629510-20% PEG4000, 0.1M cacodylic acid, 50 mM n-octyl-beta-D-glucoside, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.346.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.764α = 90
b = 74.157β = 90
c = 77.924γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 4MirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.98NSLSX4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.625.1399.70.3980.36215.81379811
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.62.6910022703

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 REPLACEMENTTHROUGHOUTPDB entry 1ZYJ2.5925.131132091899.40.229070.223060.30306RANDOM43.164
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]
-0.37-1.311.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.08
r_dihedral_angle_3_deg21.446
r_dihedral_angle_4_deg18.916
r_dihedral_angle_1_deg7.971
r_scangle_it3.403
r_scbond_it2.232
r_angle_refined_deg1.963
r_mcangle_it1.731
r_mcbond_it0.997
r_nbtor_refined0.328
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.08
r_dihedral_angle_3_deg21.446
r_dihedral_angle_4_deg18.916
r_dihedral_angle_1_deg7.971
r_scangle_it3.403
r_scbond_it2.232
r_angle_refined_deg1.963
r_mcangle_it1.731
r_mcbond_it0.997
r_nbtor_refined0.328
r_xyhbond_nbd_refined0.262
r_nbd_refined0.254
r_symmetry_vdw_refined0.194
r_chiral_restr0.134
r_bond_refined_d0.018
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2666
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms25

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling