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Human p38alpha MAP Kinase in Complex with Dibenzosuberone Compound 2
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 293 100 mM MES, 21-29 % PEG4000, 25 mM BOG
Crystal Properties Matthews coefficient Solvent content 1.95 36.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.67 α = 90 b = 69.39 β = 90 c = 70.73 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 2016-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.9893 PETRA III, DESY P11
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 2.44 49.533 99.9 0.101 10.1 5.1 13840
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 2.44 2.57 99.8 0.424 1.7 5
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 2.44 49.53 12156 591 99.84 0.18934 0.18634 0.1957 0.25381 0.2569 RANDOM 37.457
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] -1.62 3.42 -1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.054 r_dihedral_angle_4_deg 18.74 r_dihedral_angle_3_deg 16.45 r_long_range_B_refined 8.505 r_long_range_B_other 8.503 r_dihedral_angle_1_deg 6.292 r_scangle_other 4.605 r_mcangle_it 4.412 r_mcangle_other 4.411 r_scbond_it 2.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.054 r_dihedral_angle_4_deg 18.74 r_dihedral_angle_3_deg 16.45 r_long_range_B_refined 8.505 r_long_range_B_other 8.503 r_dihedral_angle_1_deg 6.292 r_scangle_other 4.605 r_mcangle_it 4.412 r_mcangle_other 4.411 r_scbond_it 2.906 r_scbond_other 2.905 r_mcbond_it 2.777 r_mcbond_other 2.774 r_angle_refined_deg 1.724 r_angle_other_deg 1.011 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 2626 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing