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Crystal Structure of Human KDM4 with Small Molecule Inhibitor QC5714
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PDQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 22% PEG4K, 100mM HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.57 52.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.14 α = 90 b = 101.429 β = 99.85 c = 142.673 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD ADSC QUANTUM 210 2016-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-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 2.48 50 99 0.127 5.7 3.7 57177
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 2.48 2.57 99.8 0.664 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3PDQ 2.48 50 54229 2904 98.68 0.1965 0.1931 0.1988 0.2599 0.262 RANDOM 41.597
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] -1.09 -1.16 1.22 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.765 r_dihedral_angle_4_deg 19.483 r_dihedral_angle_3_deg 16.423 r_dihedral_angle_1_deg 6.685 r_angle_refined_deg 1.635 r_angle_other_deg 1.013 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.765 r_dihedral_angle_4_deg 19.483 r_dihedral_angle_3_deg 16.423 r_dihedral_angle_1_deg 6.685 r_angle_refined_deg 1.635 r_angle_other_deg 1.013 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11267 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing