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A structural study of selectivity mechanisms for JNK3 and p38 alpha with indazole scaffold probing compounds
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VNX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277.15 0.2 M ammonium tartrate pH 7.2, 18 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.9 35.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.46 α = 90 b = 71.33 β = 90 c = 107.8 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 6M 2020-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.46 43.01 99.7 0.9 8.9 6.1 15534 45.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.46 2.56 0.963
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.46 42.78 15430 1199 99.22 0.1976 0.1932 0.1936 0.2504 0.2501 60.73
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.2099 f_angle_d 0.736 f_chiral_restr 0.0446 f_plane_restr 0.0055 f_bond_d 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2800 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing