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Crystal structure of JMJD5 domain of human Lysine-specific demethylase 8 (KDM8) in complex with N-oxalylglycine (NOG)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 16% PEG_3350, 0.007M NICL, 0M CDCL, 0.007M MGCL, 0.1M HEPES PH 7.3
Crystal Properties Matthews coefficient Solvent content 3.3 62.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.575 α = 90 b = 68.575 β = 90 c = 269.003 γ = 120
Symmetry Space Group P 32 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 100 CCD ADSC CCD 2011-09-22 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 2.6 19.91 99.5 0.09 10.2 7 23473 2.2 88.4
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 2.6 2.74 99.7 0.77 2.2 7.1
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 SAD THROUGHOUT NONE 2.6 89.67 22281 1210 99.61 0.20984 0.20766 0.2062 0.2529 0.249 RANDOM 65.507
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] 0.25 0.13 0.25 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.763 r_dihedral_angle_4_deg 23.232 r_dihedral_angle_3_deg 13.992 r_dihedral_angle_1_deg 6.78 r_angle_refined_deg 1.295 r_angle_other_deg 0.975 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.763 r_dihedral_angle_4_deg 23.232 r_dihedral_angle_3_deg 13.992 r_dihedral_angle_1_deg 6.78 r_angle_refined_deg 1.295 r_angle_other_deg 0.975 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 3672 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling SHARP phasing