5LAR

Crystal structure of p38 alpha MAPK14 in complex with VPC00628


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LOO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.1515% medium-molecular weight PEG Smears (MMW PEG smears), 0.1 M MES, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.2144.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.019α = 90
b = 70.58β = 90
c = 75.029γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

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
11.525.799.30.1029.75.858904
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)
11.51.5896.60.4283.14.7

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 REPLACEMENTTHROUGHOUT4LOO1.525.756060277499.170.170860.169130.20504RANDOM24.966
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]
0.91-0.28-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.431
r_dihedral_angle_4_deg16.923
r_dihedral_angle_3_deg12.62
r_long_range_B_other9.7
r_long_range_B_refined9.698
r_scangle_other8.679
r_scbond_it7.042
r_scbond_other7.04
r_mcangle_it6.42
r_mcangle_other6.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.431
r_dihedral_angle_4_deg16.923
r_dihedral_angle_3_deg12.62
r_long_range_B_other9.7
r_long_range_B_refined9.698
r_scangle_other8.679
r_scbond_it7.042
r_scbond_other7.04
r_mcangle_it6.42
r_mcangle_other6.42
r_dihedral_angle_1_deg5.441
r_mcbond_it4.903
r_mcbond_other4.901
r_angle_refined_deg1.551
r_angle_other_deg0.811
r_chiral_restr0.103
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2811
Nucleic Acid Atoms
Solvent Atoms407
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing