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Crystal structure of p38 kinase bound to pyrimido-pyridazinone inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 10 mg/mL Protein, 20 % PEG 3350, 0.1 M Tris-HCl pH 7.0, 50 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.88 57.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.697 α = 90 b = 85.958 β = 90 c = 123.271 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 110 IMAGE PLATE RIGAKU RAXIS IV 1999-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 20 95.2 0.069 8 3 18713
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 0.273 3 3
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 2.4 19.98 16861 1834 95.24 0.20401 0.1989 0.1985 0.25083 0.2487 RANDOM 34.826
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 -0.56 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.234 r_dihedral_angle_4_deg 18.42 r_dihedral_angle_3_deg 14.465 r_dihedral_angle_1_deg 5.643 r_scangle_it 1.914 r_scbond_it 1.198 r_angle_refined_deg 1.169 r_mcangle_it 0.971 r_mcbond_it 0.555 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.234 r_dihedral_angle_4_deg 18.42 r_dihedral_angle_3_deg 14.465 r_dihedral_angle_1_deg 5.643 r_scangle_it 1.914 r_scbond_it 1.198 r_angle_refined_deg 1.169 r_mcangle_it 0.971 r_mcbond_it 0.555 r_nbtor_refined 0.303 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.095 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2675 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 29
Software Software Software Name Purpose CrystalClear data collection X-PLOR model building REFMAC refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing