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Crystal structure of human JMJD2D/KDM4D in complex with an H3K9me3 peptide and 2-oxoglutarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q8C PDB ENTRY 2Q8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 7% PEG 3350, 0.1M sodium thiocyanate, 0.35M potassium nitrate, vapor diffusion, hanging drop, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 3.23 61.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.202 α = 90 b = 79.675 β = 90 c = 175.938 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 300 mm CCD 2010-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
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 1.799 25 94.5 0.082 9.5 13.7 89438
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 1.799 1.84 100 0.455 10.6 6206
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 PDB ENTRY 2Q8C 1.799 24.93 89102 4486 93.93 0.1905 0.1892 0.1894 0.2143 0.2126 RANDOM 20.5226
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] 0.09 -0.73 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.317 r_dihedral_angle_4_deg 16.46 r_dihedral_angle_3_deg 11.555 r_dihedral_angle_1_deg 5.964 r_scangle_it 3.857 r_scbond_it 2.442 r_mcangle_it 1.554 r_angle_refined_deg 1.434 r_mcbond_it 0.865 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.317 r_dihedral_angle_4_deg 16.46 r_dihedral_angle_3_deg 11.555 r_dihedral_angle_1_deg 5.964 r_scangle_it 3.857 r_scbond_it 2.442 r_mcangle_it 1.554 r_angle_refined_deg 1.434 r_mcbond_it 0.865 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5398 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 115
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction CCP4 phasing