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Crystal structure of human KDM4C catalytic domain with OGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291.15 0.8 M Lithium chloride, 0.1 M Tris pH 8.5, 28 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.62 52.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.93 α = 90 b = 89.77 β = 96.49 c = 98.46 γ = 90
Symmetry Space Group C 1 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 MARMOSAIC 300 mm CCD 2013-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.97 40.8 99.9 0.098 0.054 0.996 12 4.2 57310
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.02 99.8 0.604 0.366 0.696 2.2 3.7 4194
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.97 40.58 54401 2906 99.83 0.2032 0.2004 0.2071 0.254 0.2607 RANDOM 24.476
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.167 r_dihedral_angle_3_deg 15.418 r_dihedral_angle_4_deg 14.864 r_dihedral_angle_1_deg 6.615 r_mcangle_it 3.193 r_mcbond_it 2.214 r_mcbond_other 2.213 r_angle_refined_deg 1.9 r_angle_other_deg 0.916 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.167 r_dihedral_angle_3_deg 15.418 r_dihedral_angle_4_deg 14.864 r_dihedral_angle_1_deg 6.615 r_mcangle_it 3.193 r_mcbond_it 2.214 r_mcbond_other 2.213 r_angle_refined_deg 1.9 r_angle_other_deg 0.916 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5548 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing