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Crystal structure of human KDM2A with substrate competitive inhibitor 183c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YU1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 19% PEG 2000 MME, 0.1M Tris pH 8.0, 0.2M TMANO, 8% glycerol
Crystal Properties Matthews coefficient Solvent content 2.33 44.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.374 α = 90 b = 81.374 β = 90 c = 124.023 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS PILATUS 6M 2019-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.48310 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.16 70.47 98.37 0.061 0.998 14.38 4.58 47966 49.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.16 2.29 83.5 0.567 0.715 1.28 2.13
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.16 70.47 1.36 25647 1286 98.37 0.1807 0.179 0.1793 0.2115 0.2117 59.23
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 14.1639 f_angle_d 0.6913 f_chiral_restr 0.0468 f_bond_d 0.0048 f_plane_restr 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3134 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing