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Crystal Structure of Human P38 alpha MAPK in Complex with MW01-21-114SRM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EWQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 Protein: 9.2 mg/ml, 0.15M Sodium chloride, 0.02M Tris-HCl (pH 8.3), 1mM TCEP;
Screen: 0.1M Ammomium acetate, 0.1M Bis-Tris (pH 5.5), 17% (w/v) PEG10000, 2mM 4FPP (4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]pyridine);
Soak: 24 hrs, 5mM ligand (MW01-25-195SRM) in screen solution;
Cryo: 0.1M Bis-Tris (pH 5.5), 20% (w/v) PEG10000
Crystal Properties Matthews coefficient Solvent content 2.4 48.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.074 α = 90 b = 74.8 β = 90 c = 78.662 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2025-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.05 30 100 0.067 0.067 0.072 0.026 0.998 33.2 7.8 25632 -3 38.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 100 0.473 0.723 1.8 8.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.05 28.21 23700 1274 99.52 0.1934 0.19099 0.2017 0.23604 0.2385 RANDOM 50.663
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] 2.98 -1.25 -1.72
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 10.982 r_long_range_B_other 10.966 r_scangle_other 8.421 r_dihedral_angle_3_deg 8.103 r_scbond_it 6.095 r_scbond_other 6.093 r_mcangle_it 6.033 r_mcangle_other 6.032 r_mcbond_it 4.514 r_mcbond_other 4.512
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 10.982 r_long_range_B_other 10.966 r_scangle_other 8.421 r_dihedral_angle_3_deg 8.103 r_scbond_it 6.095 r_scbond_other 6.093 r_mcangle_it 6.033 r_mcangle_other 6.032 r_mcbond_it 4.514 r_mcbond_other 4.512 r_dihedral_angle_2_deg 2.885 r_dihedral_angle_1_deg 2.794 r_angle_refined_deg 1.725 r_angle_other_deg 0.552 r_chiral_restr 0.089 r_gen_planes_refined 0.02 r_gen_planes_other 0.016 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 Atoms Number Protein Atoms 2693 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling REFMAC phasing