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Cell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) families of histone lysine demethylases
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.1M TRIS HCL, BICINE PH 8.5, 37.5% MPD, PEG1K, PEG3350, 0.03M MGCL2, 0.03M CACL2
Crystal Properties Matthews coefficient Solvent content 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.199 α = 85.59 b = 65.552 β = 67.65 c = 77.301 γ = 68.39
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2010-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF ESRF
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 2.05 40 96 0.07 11.4 2.1 61615 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 2.05 2.09 90.3 0.32 2.2 2
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 NONE 2.05 71.3 59141 2470 95.7 0.20622 0.20464 0.2086 0.24322 0.248 RANDOM 25.083
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] 0.11 -2.17 -1.27 1.89 3.03 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.377 r_dihedral_angle_3_deg 10.313 r_dihedral_angle_4_deg 8.036 r_dihedral_angle_1_deg 4.467 r_angle_refined_deg 0.818 r_angle_other_deg 0.73 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.377 r_dihedral_angle_3_deg 10.313 r_dihedral_angle_4_deg 8.036 r_dihedral_angle_1_deg 4.467 r_angle_refined_deg 0.818 r_angle_other_deg 0.73 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6836 Nucleic Acid Atoms Solvent Atoms 835 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement HKL data reduction SCALEPACK data scaling