3MPA

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% PEG 4000, 0.1 M cacodylic acid, 50 mM n-octyl-beta-D-glucoside, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2745.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.471α = 90
b = 74.144β = 90
c = 77.184γ = 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
12.140950.0420.03131225301
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.1879.60.2660.2362.92.41755

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 1ZYJ2.130.3420146169197.110.235020.230430.28933RANDOM36.33
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]
0.1-1.321.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.132
r_dihedral_angle_3_deg20.188
r_dihedral_angle_4_deg19.341
r_dihedral_angle_1_deg6.552
r_scangle_it3
r_scbond_it1.984
r_mcangle_it1.55
r_angle_refined_deg1.467
r_mcbond_it0.89
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.132
r_dihedral_angle_3_deg20.188
r_dihedral_angle_4_deg19.341
r_dihedral_angle_1_deg6.552
r_scangle_it3
r_scbond_it1.984
r_mcangle_it1.55
r_angle_refined_deg1.467
r_mcbond_it0.89
r_nbtor_refined0.309
r_symmetry_vdw_refined0.225
r_nbd_refined0.217
r_symmetry_hbond_refined0.176
r_xyhbond_nbd_refined0.168
r_chiral_restr0.102
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2674
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms47

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling