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Crystal structure of human KDM4D in complex with 2-1H-pyrazol-4-yloxy- 3H,4H-pyrido-3,4-d-pyrimidin-4-one
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 0.1M HEPES PH 7.4, 2.45M AMMONIUM SULPHATE
Crystal Properties Matthews coefficient Solvent content 2.48 50.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.18 α = 90 b = 71.18 β = 90 c = 150.788 γ = 90
Symmetry Space Group P 43 21 2
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 RIGAKU SATURN A200 2012-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT
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 1.91 41.86 99.6 0.06 18.8 4.7 30844 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 1.91 2.01 99.8 0.42 3.9 3.9
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 1.91 31.15 29158 1550 99.3 0.16243 0.16035 0.1716 0.20319 0.2131 RANDOM 25.725
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] 0.51 0.51 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.856 r_dihedral_angle_4_deg 18.088 r_dihedral_angle_3_deg 12.275 r_dihedral_angle_1_deg 5.367 r_mcangle_it 1.938 r_scbond_it 1.637 r_mcbond_it 1.16 r_mcbond_other 1.158 r_angle_refined_deg 1.009 r_angle_other_deg 0.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.856 r_dihedral_angle_4_deg 18.088 r_dihedral_angle_3_deg 12.275 r_dihedral_angle_1_deg 5.367 r_mcangle_it 1.938 r_scbond_it 1.637 r_mcbond_it 1.16 r_mcbond_other 1.158 r_angle_refined_deg 1.009 r_angle_other_deg 0.712 r_chiral_restr 0.063 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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_mcangle_other 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 2682 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling