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Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 273 25% PEG 4000, 100mM HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.52 51.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.318 α = 90 b = 101.594 β = 99.64 c = 141.893 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 4 2016-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 1 APS 14-BM-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.08 50 88.4 0.053 0.07 0.046 8 1.9 85582
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 2.08 2.15 90.2 0.388 0.517 0.338 0.726 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 2.07 50 81279 4274 87.88 0.1918 0.1888 0.2485 0.2506 RANDOM 37.281
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] -0.56 -0.4 0.92 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.052 r_dihedral_angle_4_deg 18.549 r_dihedral_angle_3_deg 18.089 r_dihedral_angle_1_deg 7.443 r_angle_refined_deg 2.312 r_chiral_restr 0.163 r_bond_refined_d 0.025 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11288 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-3000 data collection