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Structure of histone lysine demethylase KDM5A in complex with selective inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% PEG3350, 0.1 M HEPES, pH 7.3, 12% glycerol
Crystal Properties Matthews coefficient Solvent content 3.73 67.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.306 α = 90 b = 159.306 β = 90 c = 92.462 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 93 CCD RAYONIX MX300HE 2013-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 3.1 40 96.8 0.136 6.5 5.3 23075 108.1
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 3.1 3.21 94.6 0.82 0.915 0.397 0.56 4.7 2205
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.14 39.83 1.37 23004 1162 96 0.222 0.221 0.223 0.238 0.2378 Random selection 70.02
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 16.151 f_angle_d 1.297 f_chiral_restr 0.064 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4641 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction