☰ Navigation Tabs
Human p38alpha MAP Kinase in complex with (Naphthalen-1-yl)pyridazine derivative GDK767-7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EWQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 0.1M Ammonium Acetate, 0.1< BisTris (pH 5.5), 20% PEG 10,000
Crystal Properties Matthews coefficient Solvent content 2.33 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.758 α = 90 b = 74.556 β = 90 c = 80.161 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 EIGER2 X 9M Vertical CRL / Horizontal Eliptical mirror 2023-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
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 2.13 54.59 99.8 0.109 0.116 0.045 0.998 13.3 13 23281 50.37
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 2.13 2.19 98.7 2.353 2.535 0.942 0.59 1.3 13.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.13 54.59 1.34 23222 1103 99.75 0.2135 0.2445 0.2419 Random 78.49
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 6.2263 f_angle_d 0.5894 f_chiral_restr 0.0396 f_plane_restr 0.0082 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2706 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement Aimless data scaling