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Covalent Inhibitor 4b bound to the Lipid Pocket of p38alpha Mutant S252C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 100 mM MES pH 5.6-6.2
20-30 % PEG4000
Crystal Properties Matthews coefficient Solvent content 2.32 47.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.58 α = 90 b = 74.05 β = 90 c = 76.71 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 90 PIXEL DECTRIS PILATUS 6M-F 2016-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00601 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 50 100 0.154 14.42 12.89 25307
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99.7 0.908 2.64 11.16
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 4DLI 2 41.84 25307 1332 99.97 0.20518 0.20264 0.2103 0.25236 0.253 RANDOM 34.502
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] 0.15 -1.44 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.217 r_dihedral_angle_4_deg 19.515 r_dihedral_angle_3_deg 15.748 r_long_range_B_refined 7.529 r_long_range_B_other 7.518 r_dihedral_angle_1_deg 5.573 r_scangle_other 5.17 r_mcangle_it 4.164 r_mcangle_other 4.163 r_scbond_it 3.455
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.217 r_dihedral_angle_4_deg 19.515 r_dihedral_angle_3_deg 15.748 r_long_range_B_refined 7.529 r_long_range_B_other 7.518 r_dihedral_angle_1_deg 5.573 r_scangle_other 5.17 r_mcangle_it 4.164 r_mcangle_other 4.163 r_scbond_it 3.455 r_scbond_other 3.454 r_mcbond_it 2.863 r_mcbond_other 2.86 r_angle_refined_deg 1.699 r_angle_other_deg 1.071 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2615 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing