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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 1OVE PDB ENTRY 1OVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 22% PEG3350, 0.2 M sodium chloride, 0.1 M Bis-Tris, pH 6.5, 1 mM THP, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.97 58.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.28 α = 90 b = 84.96 β = 90 c = 123.51 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++ 2006-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 1.8 29.566 92.9 0.102 4.34 45003 41810
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 1.8 1.86 89.2 0.61 3.42
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OVE 1.8 29.566 41810 2092 92.9 0.2328 0.2294 0.2337 0.2576 0.2955 RANDOM 43.23
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] -0.03 -0.07 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.492 r_dihedral_angle_4_deg 19.978 r_dihedral_angle_3_deg 17.568 r_dihedral_angle_1_deg 8.031 r_scangle_it 4.827 r_scbond_it 3.127 r_mcangle_it 2.291 r_angle_refined_deg 2.041 r_mcbond_it 1.37 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.492 r_dihedral_angle_4_deg 19.978 r_dihedral_angle_3_deg 17.568 r_dihedral_angle_1_deg 8.031 r_scangle_it 4.827 r_scbond_it 3.127 r_mcangle_it 2.291 r_angle_refined_deg 2.041 r_mcbond_it 1.37 r_nbtor_refined 0.317 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.217 r_symmetry_hbond_refined 0.202 r_symmetry_vdw_refined 0.162 r_chiral_restr 0.128 r_bond_refined_d 0.021 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2800 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction CrystalClear data scaling Coot model building MOLREP phasing