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Crystal structure of MAP kinase p38 alpha in complex with inhibitor SR159
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LAR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 20% MMW PEG smear, 0.1M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.36 47.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.46 α = 90 b = 75.24 β = 90 c = 78.19 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 PILATUS3 6M 2017-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91840 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 78.19 98.2 0.062 0.994 7.3 3.3 23058 37.3277444709
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 98.8 0.42 0.747 2.6 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5LAR 2.1 50.6389 1.33416417525 22769 1137 96.8110889068 0.21718782692 0.214513173644 0.2201 0.267854803463 0.2673 52.3287626909
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 16.9382481495 f_angle_d 1.00642121681 f_chiral_restr 0.0612913602103 f_bond_d 0.00840592134494 f_plane_restr 0.0059515979759
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2580 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 47
Software Software Software Name Purpose PHENIX refinement PHASER phasing