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Crystal structure of p38 alpha in complex with compound 75 (MCP33)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LAR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 277.15 25% MMW PEG smears, 0.1M MES pH 6.2
Crystal Properties Matthews coefficient Solvent content 2.28 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.449 α = 90 b = 71.289 β = 90 c = 76.2 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 PIXEL DECTRIS PILATUS 2M-F 2016-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.6 52.06 99.8 0.062 0.073 0.027 0.999 15.6 6.8 50532
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 99.8 0.6 0.7 0.259 0.794 7.1
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 5LAR 1.6 52.06 48070 2402 99.71 0.1764 0.175 0.1871 0.2025 0.213 RANDOM 23.891
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] 0.53 -0.28 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.775 r_dihedral_angle_4_deg 15.63 r_dihedral_angle_3_deg 12.793 r_dihedral_angle_1_deg 6.453 r_angle_refined_deg 1.589 r_angle_other_deg 1.391 r_chiral_restr 0.086 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.775 r_dihedral_angle_4_deg 15.63 r_dihedral_angle_3_deg 12.793 r_dihedral_angle_1_deg 6.453 r_angle_refined_deg 1.589 r_angle_other_deg 1.391 r_chiral_restr 0.086 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2738 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 36
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing