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The third conformation of p38a MAP kinase observed in phosphorylated p38a and in solution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LEZ PDB ENTRY 1LEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 1.45M (NH4)2SO4, 0.2M Li2SO4, 0.1M Hepes pH 7.0-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.79 55.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.641 α = 90 b = 82.641 β = 90 c = 123.64 γ = 120
Symmetry Space Group P 31 2 1
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 ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97905 APS 19-ID
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 2.3 50 99.9 0.072 20.7 6.6 22102 22102
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1LEZ 2.304 46.78 20973 1129 99.81 0.17882 0.17565 0.23937 0.2182 RANDOM 31.265
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] -0.02 -0.01 -0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.804 r_dihedral_angle_4_deg 21.061 r_dihedral_angle_3_deg 17.351 r_dihedral_angle_1_deg 7.073 r_scangle_it 5.704 r_scbond_it 3.537 r_mcangle_it 2.413 r_angle_refined_deg 1.927 r_mcbond_it 1.26 r_chiral_restr 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.804 r_dihedral_angle_4_deg 21.061 r_dihedral_angle_3_deg 17.351 r_dihedral_angle_1_deg 7.073 r_scangle_it 5.704 r_scbond_it 3.537 r_mcangle_it 2.413 r_angle_refined_deg 1.927 r_mcbond_it 1.26 r_chiral_restr 0.145 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2806 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling