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Human p38 ALPHA MAPK:MW164 pyridazine inhibitor complex
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 5.5 292 Protein: 20.0 mg/ml, 0.15M Sodium chloride, 0.02M Tris-HCl (pH 8.3), 1mM TCEP; Screen: 0.15M Ammomium acetate, 0.1M Bis-Tris (pH 5.5), 16% (w/v) PEG1000; Soak: 24 hrs, 5mM ligand in screen solution; Cryo: 10% Glycerol in screen solution.
Crystal Properties Matthews coefficient Solvent content 2.41 49.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.039 α = 90 b = 74.757 β = 90 c = 79.51 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 PIXEL DECTRIS EIGER X 9M KB bimorph mirrors 2023-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92010 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.97 79.51 97.2 0.116 0.123 0.04 0.815 13.2 9.9 28061 29.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.08 95.9 1.208 1.329 0.503 2.3 9.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1.97 49.91 1.34 27964 1412 97.01 0.1831 0.1813 0.1873 0.2208 0.2205 Random selection
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.83 f_angle_d 0.782 f_chiral_restr 0.046 f_plane_restr 0.007 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2726 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 65
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction autoPROC data reduction REFMAC phasing