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Crystal structure of JmjC domain of human histone demethylase UTY in complex with epitherapuetic compound 2-(((2-((2-(dimethylamino)ethyl) (ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinic acid.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZLI PDB ENTRY 3ZLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 25% PEG3350, 0.1M BIS-TRIS PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.83 56.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.494 α = 90 b = 110.458 β = 90 c = 119.23 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 CCD ADSC CCD ADSC QUANTUM 315 2014-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.78 81.03 99.9 0.06 19.51 6.7 114771 2
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 1.78 1.84 99.9 0.06 2.86 6.8
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 PDB ENTRY 3ZLI 1.78 81.03 109117 5650 99.97 0.15184 0.14857 0.1615 0.21517 0.2263 RANDOM 36.64
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] -1.63 0.49 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.489 r_sphericity_free 28.313 r_sphericity_bonded 18.008 r_dihedral_angle_4_deg 15.561 r_dihedral_angle_3_deg 13.89 r_scbond_it 7.072 r_dihedral_angle_1_deg 6.389 r_mcangle_it 6.02 r_rigid_bond_restr 5.478 r_mcbond_it 5.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.489 r_sphericity_free 28.313 r_sphericity_bonded 18.008 r_dihedral_angle_4_deg 15.561 r_dihedral_angle_3_deg 13.89 r_scbond_it 7.072 r_dihedral_angle_1_deg 6.389 r_mcangle_it 6.02 r_rigid_bond_restr 5.478 r_mcbond_it 5.359 r_mcbond_other 5.358 r_angle_refined_deg 1.714 r_angle_other_deg 0.909 r_chiral_restr 0.101 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7058 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling CCP4I phasing