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p38 kinase Crystal structure in complex with small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A9U PDB ENTRY 1A9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 22% PEG 3350, 0.2M NaCl, 0.1M Bis-Tris pH 6.5, 1mM THP, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.91 57.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.22 α = 90 b = 86.75 β = 90 c = 122.23 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 2005-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54180
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 2.2 70.744 84.2 0.057 0.057 9.5 1.9 40419 20806 35.9
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) 2.2 2.32 89.1 0.367 0.367 2.2 1.8 5586
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1A9U 2.2 29.7 40419 19725 1072 82.58 0.217 0.214 0.218 0.26 0.2636 RANDOM 26.83
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] -0.44 -0.77 1.2
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 2.402 p_scbond_it 1.441 p_mcangle_it 1.333 p_angle_d 1.202 p_mcbond_it 0.718 p_chiral_restr 0.071 p_bond_d 0.01 p_plane_restr 0.005 p_angle_deg p_planar_d
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 2.402 p_scbond_it 1.441 p_mcangle_it 1.333 p_angle_d 1.202 p_mcbond_it 0.718 p_chiral_restr 0.071 p_bond_d 0.01 p_plane_restr 0.005 p_angle_deg p_planar_d p_hb_or_metal_coord p_singtor_nbd p_multtor_nbd p_xhyhbond_nbd p_xyhbond_nbd p_planar_tor p_staggered_tor p_orthonormal_tor p_transverse_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2766 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 25
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction