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Crystal Structure of P38 Kinase in Complex with A Biaryl Amide Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WFC PDB ENTRY 1WFC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 18-22% PEG 5000MME, 0.18M ammonium sulphate, 3-4% jeffamine, 0.1M ADA, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.91 57.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.768 α = 90 b = 86.044 β = 90 c = 126.285 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 IMAGE PLATE RIGAKU RAXIS IV++ MIRRORS 2001-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R 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 35 91.8 0.076 14.1 31814 28
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 2.07 89.2 0.506 0.506 2.1 3042
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1WFC 2 20 31676 1598 100 0.171 0.169 0.1734 0.228 0.2339 RANDOM 37.073
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] -0.71 0.32 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.268 r_dihedral_angle_4_deg 19.84 r_dihedral_angle_3_deg 13.546 r_dihedral_angle_1_deg 9.785 r_scangle_it 3.897 r_scbond_it 2.749 r_mcangle_it 1.771 r_angle_refined_deg 1.244 r_mcbond_it 1.103 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.268 r_dihedral_angle_4_deg 19.84 r_dihedral_angle_3_deg 13.546 r_dihedral_angle_1_deg 9.785 r_scangle_it 3.897 r_scbond_it 2.749 r_mcangle_it 1.771 r_angle_refined_deg 1.244 r_mcbond_it 1.103 r_nbtor_refined 0.304 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2800 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 55
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing