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A Novel Lipid Binding Site in the p38 alpha MAP Kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FSO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.25 277 15% PEG 3350, 0.2M KF, 0.1M Hepes pH 7.25, 25mM BOG, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.25 45.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.607 α = 90 b = 74.212 β = 90 c = 74.571 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 2006-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 33.15 0.06 33 4.6 37500 36965
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.83 0.601 1.6
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2FSO 1.8 32.76 33741 1788 98.79 0.20541 0.20332 0.24473 RANDOM 30
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] -0.01 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.254 r_scangle_it 4.344 r_scbond_it 2.646 r_mcangle_it 1.967 r_angle_refined_deg 1.589 r_mcbond_it 1.086 r_angle_other_deg 0.881 r_symmetry_vdw_other 0.265 r_nbd_other 0.234 r_nbd_refined 0.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.254 r_scangle_it 4.344 r_scbond_it 2.646 r_mcangle_it 1.967 r_angle_refined_deg 1.589 r_mcbond_it 1.086 r_angle_other_deg 0.881 r_symmetry_vdw_other 0.265 r_nbd_other 0.234 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.163 r_symmetry_vdw_refined 0.155 r_chiral_restr 0.115 r_nbtor_other 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2643 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling