3MW1

p38 kinase Crystal structure in complex with small molecule inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529822% PEG 3350, 0.2M NaCl, 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9458.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.26α = 90
b = 87.23β = 90
c = 122.81γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
12.82090.10.1111267
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)
12.82.998.40.3772.92

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 3HRB2.819.931126754790.120.259020.255160.33907RANDOM40.425
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]
-0.410.270.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.153
r_dihedral_angle_4_deg21.485
r_dihedral_angle_3_deg18.706
r_dihedral_angle_1_deg6.228
r_scangle_it1.623
r_angle_refined_deg1.199
r_scbond_it0.927
r_mcangle_it0.857
r_angle_other_deg0.855
r_mcbond_it0.455
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.153
r_dihedral_angle_4_deg21.485
r_dihedral_angle_3_deg18.706
r_dihedral_angle_1_deg6.228
r_scangle_it1.623
r_angle_refined_deg1.199
r_scbond_it0.927
r_mcangle_it0.857
r_angle_other_deg0.855
r_mcbond_it0.455
r_chiral_restr0.062
r_mcbond_other0.053
r_bond_refined_d0.01
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2725
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction