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Crystal structure of human KDM4C catalytic domain bound to tris
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 2.61 52.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.87 α = 90 b = 89.75 β = 96.31 c = 98.28 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 2.07 31.42 98.6 0.124 0.068 0.995 11 4.3 48744
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 2.07 2.12 97.8 0.669 0.366 0.733 2.3 4.3 3558
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 MOLECULAR REPLACEMENT THROUGHOUT 2.07 31.42 48738 2463 98.55 0.2084 0.2066 0.2139 0.242 0.2467 RANDOM 27.402
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] 0.86 0.3 -0.36 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.83 r_dihedral_angle_3_deg 14.93 r_dihedral_angle_4_deg 14.778 r_dihedral_angle_1_deg 6.212 r_angle_refined_deg 1.367 r_mcangle_it 0.936 r_angle_other_deg 0.767 r_mcbond_it 0.523 r_mcbond_other 0.522 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.83 r_dihedral_angle_3_deg 14.93 r_dihedral_angle_4_deg 14.778 r_dihedral_angle_1_deg 6.212 r_angle_refined_deg 1.367 r_mcangle_it 0.936 r_angle_other_deg 0.767 r_mcbond_it 0.523 r_mcbond_other 0.522 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 317 Heterogen Atoms 73
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing