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p38(alpha) MAP kinase with the activation loop of ERK2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other p38 wild type
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M HEPES pH 7.5,
0.2 M KF,
13%-17% (w/v) PEG 3350,
25 mM beta-D-octyl glucoside (bOG)
Crystal Properties Matthews coefficient Solvent content 2.3 46.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.86 α = 90 b = 74.5 β = 90 c = 75.28 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 2M 2015-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.66 52.95 99.1 0.068 9.8 4.2 46102
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.72 0.862
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 p38 wild type 1.66 52.95 43882 2168 99.14 0.18774 0.18485 0.1888 0.24233 0.2508 RANDOM 37.548
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] -2.4 4.29 -1.9
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.502 r_dihedral_angle_2_deg 33.25 r_sphericity_bonded 27.03 r_dihedral_angle_4_deg 21.886 r_dihedral_angle_3_deg 16.994 r_long_range_B_refined 10.335 r_long_range_B_other 10.326 r_scangle_other 9.624 r_mcangle_it 8.337 r_mcangle_other 8.335
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.502 r_dihedral_angle_2_deg 33.25 r_sphericity_bonded 27.03 r_dihedral_angle_4_deg 21.886 r_dihedral_angle_3_deg 16.994 r_long_range_B_refined 10.335 r_long_range_B_other 10.326 r_scangle_other 9.624 r_mcangle_it 8.337 r_mcangle_other 8.335 r_scbond_it 7.851 r_scbond_other 7.85 r_dihedral_angle_1_deg 6.785 r_mcbond_it 6.736 r_mcbond_other 6.726 r_rigid_bond_restr 3.064 r_angle_refined_deg 1.804 r_angle_other_deg 0.908 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2731 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing