1W84

p38 Kinase crystal structure in complex with small molecule inhibitor


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.9958.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.639α = 90
b = 86.604β = 90
c = 124.921γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100MIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
12.25093.90.0712.52.3242072

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONOTHERTHROUGHOUT2.219.572296812361000.1820.1790.238RANDOM22.24
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]
-0.190.31-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.454
r_dihedral_angle_4_deg20.389
r_dihedral_angle_3_deg14.78
r_dihedral_angle_1_deg6.518
r_scangle_it3.261
r_mcangle_it3.19
r_mcbond_it2.822
r_scbond_it2.501
r_angle_refined_deg1.592
r_angle_other_deg1.394
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.454
r_dihedral_angle_4_deg20.389
r_dihedral_angle_3_deg14.78
r_dihedral_angle_1_deg6.518
r_scangle_it3.261
r_mcangle_it3.19
r_mcbond_it2.822
r_scbond_it2.501
r_angle_refined_deg1.592
r_angle_other_deg1.394
r_mcbond_other0.877
r_nbtor_refined0.152
r_nbd_refined0.145
r_nbd_other0.098
r_symmetry_vdw_other0.095
r_chiral_restr0.094
r_xyhbond_nbd_refined0.082
r_nbtor_other0.077
r_symmetry_hbond_refined0.062
r_symmetry_vdw_refined0.045
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.003
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2834
Nucleic Acid Atoms
Solvent Atoms576
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement