4ZTH

Structure of human p38aMAPK-arylpyridazinylpyridine fragment complex used in inhibitor discovery


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52950.1M Ammonium Acetate, 0.1 BisTris (pH 5.5), 17% PEG 10,000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1643.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.767α = 90
b = 74.501β = 90
c = 77.669γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
12.153099.80.06424.14.820253
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)
12.152.191000.6524.9

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.153020253103699.80.1840.1810.24RANDOM48.68
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]
1.12-0.26-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.887
r_dihedral_angle_4_deg14.927
r_dihedral_angle_3_deg13.175
r_long_range_B_refined8.381
r_long_range_B_other8.365
r_scangle_other5.976
r_mcangle_it4.85
r_mcangle_other4.849
r_dihedral_angle_1_deg3.978
r_scbond_it3.821
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.887
r_dihedral_angle_4_deg14.927
r_dihedral_angle_3_deg13.175
r_long_range_B_refined8.381
r_long_range_B_other8.365
r_scangle_other5.976
r_mcangle_it4.85
r_mcangle_other4.849
r_dihedral_angle_1_deg3.978
r_scbond_it3.821
r_scbond_other3.809
r_mcbond_it3.353
r_mcbond_other3.352
r_angle_refined_deg1.687
r_angle_other_deg0.937
r_chiral_restr0.103
r_gen_planes_refined0.027
r_gen_planes_other0.021
r_bond_refined_d0.016
r_bond_other_d0.002
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 Atoms2736
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing