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Crystal structure of p38 alpha MAP kinase in complex with a novel isoform selective drug candidate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 0.075M Ammonium Acetate, 0.1M BisTris (pH 5.5), 16% PEG 10000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.17 43.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.85 α = 90 b = 74.512 β = 90 c = 77.808 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 CCD MARMOSAIC 225 mm CCD Beryllium lenses 2013-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.05 30 100 0.062 0.062 23.17 4.8 24314 -3 35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 100 0.599 0.599 2.37 4.9 1188
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 (All) 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 PDB entry 4F9W THROUGHOUT 2.06 29.93 23018 1241 99.12 0.17761 0.17761 0.1755 0.1835 0.21669 0.2226 RANDOM 46.096
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] -1.46 -1.49 2.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.021 r_dihedral_angle_4_deg 12.783 r_dihedral_angle_3_deg 9.888 r_long_range_B_refined 7.046 r_long_range_B_other 7.02 r_scangle_other 4.674 r_mcangle_it 3.437 r_mcangle_other 3.436 r_scbond_it 2.953 r_scbond_other 2.952
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.021 r_dihedral_angle_4_deg 12.783 r_dihedral_angle_3_deg 9.888 r_long_range_B_refined 7.046 r_long_range_B_other 7.02 r_scangle_other 4.674 r_mcangle_it 3.437 r_mcangle_other 3.436 r_scbond_it 2.953 r_scbond_other 2.952 r_dihedral_angle_1_deg 2.618 r_mcbond_other 2.302 r_mcbond_it 2.301 r_angle_refined_deg 1.397 r_angle_other_deg 0.708 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2720 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 77
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling