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Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4-difluoropiperidin-1-yl)ethyl]-5-fluoro-1H-indazol-3-yl}amino)pyridine-4-carboxylic acid]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E6H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 1.2-1.35 M (NH4)2SO4,
0.1 M Tris-HCl (pH 8.6-9.2)
0-20% glycerol
25 mM (Na/K) dibasic/monobasic phosphate
Crystal Properties Matthews coefficient Solvent content 2.24 45.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.556 α = 90 b = 62.516 β = 92.32 c = 46.772 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2015-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.569 32.979 99.7 0.12 17.6 7.2 46861
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 1.569 1.61 96.8 0.885 2.3 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5E6H 1.569 32.979 1.35 46849 1980 99.6 0.1602 0.1589 0.1894 0.2075
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 16.849 f_angle_d 1.208 f_chiral_restr 0.084 f_bond_d 0.015 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2333 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing