3OBG

Conformational plasticity of p38 MAP kinase DFG 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 DROP629510-15% PEG 4000, 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
2.2445.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.118α = 90
b = 73.697β = 90
c = 77.08γ = 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
12.830.2599.10.1430.10911.3956311
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.83.0299.82.21847

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 1ZYJ2.830.25873371298.520.222160.213980.32284RANDOM37.858
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]
0.46-2.722.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.685
r_dihedral_angle_4_deg26.898
r_dihedral_angle_3_deg23.541
r_dihedral_angle_1_deg9.066
r_scangle_it3.824
r_scbond_it2.385
r_angle_refined_deg2.246
r_mcangle_it1.742
r_mcbond_it1.01
r_nbtor_refined0.341
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.685
r_dihedral_angle_4_deg26.898
r_dihedral_angle_3_deg23.541
r_dihedral_angle_1_deg9.066
r_scangle_it3.824
r_scbond_it2.385
r_angle_refined_deg2.246
r_mcangle_it1.742
r_mcbond_it1.01
r_nbtor_refined0.341
r_nbd_refined0.286
r_symmetry_vdw_refined0.259
r_xyhbond_nbd_refined0.194
r_chiral_restr0.133
r_symmetry_hbond_refined0.124
r_bond_refined_d0.023
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2675
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms27

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling