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Crystal structure of P38 kinase in complex with a biphenyl 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 Authors suggest to see publication for details, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.07 59.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.24 α = 90 b = 86.523 β = 90 c = 127.108 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 ADSC QUANTUM 4 2001-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.87000 SRS PX9.6
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 1.9 35 82.4 0.053 12.9 34124 25.7
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 1.9 1.97 72.2 0.524 1.7 2939
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 1.9 20 33850 1712 100 0.177 0.175 0.177 0.218 0.2189 RANDOM 35.516
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] 0.34 -0.51 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.542 r_dihedral_angle_4_deg 18.378 r_dihedral_angle_3_deg 14.665 r_dihedral_angle_1_deg 13.368 r_scangle_it 4.436 r_scbond_it 3.148 r_mcangle_it 1.995 r_angle_refined_deg 1.378 r_mcbond_it 1.293 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.542 r_dihedral_angle_4_deg 18.378 r_dihedral_angle_3_deg 14.665 r_dihedral_angle_1_deg 13.368 r_scangle_it 4.436 r_scbond_it 3.148 r_mcangle_it 1.995 r_angle_refined_deg 1.378 r_mcbond_it 1.293 r_nbtor_refined 0.301 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.199 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.094 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2819 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 41
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection REFMAC phasing