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Structure of p38 alpha (Mitogen-activated protein kinase 14) complexed with inhibitor 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HV7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 277 10% PEG6000, 0.1 MES/NaOH pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.15 42.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.124 α = 90 b = 74.341 β = 90 c = 78.029 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 PILATUS 6M 2018-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99997 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.85 49.46 97.4 0.027999999999999997 0.033 0.9990000000000001 24.04 3.7 32652
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 2.1 0.46 0.534 0.932
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 1.85 49.46 29677 2236 95.23 0.2228 0.2179 0.2265 0.28853 0.2941 RANDOM 46.929
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] 0.11 -2.35 2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.931 r_dihedral_angle_4_deg 17.19 r_dihedral_angle_3_deg 15.186 r_long_range_B_other 13.639 r_long_range_B_refined 13.621 r_scangle_other 12.674 r_mcangle_other 10.758 r_mcangle_it 10.748 r_scbond_it 10.39 r_scbond_other 10.386
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.931 r_dihedral_angle_4_deg 17.19 r_dihedral_angle_3_deg 15.186 r_long_range_B_other 13.639 r_long_range_B_refined 13.621 r_scangle_other 12.674 r_mcangle_other 10.758 r_mcangle_it 10.748 r_scbond_it 10.39 r_scbond_other 10.386 r_mcbond_it 9.055 r_mcbond_other 9.022 r_dihedral_angle_1_deg 6.342 r_angle_refined_deg 1.359 r_angle_other_deg 0.449 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 2653 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 44
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PHASER phasing