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Crystal structure of JMJD2A complexed with histone H3 peptide trimethylated at Lys36
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OQ7 PDB entry 2oq7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 20% PEG 3350, 0.1 M Citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.35 47.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.943 α = 90 b = 148.886 β = 90 c = 56.975 γ = 90
Symmetry Space Group P 21 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 IMAGE PLATE RIGAKU RAXIS HTC 2007-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54180
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 2.3 30 98.4 0.059 20 3.8 38324 38324 47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 93.3 1.9 3.6 5187
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB entry 2oq7 2.3 30 36665 36665 1608 98.17 0.17863 0.17863 0.17649 0.1798 0.22552 0.2261 RANDOM 29.484
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] -1.17 0.07 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.405 r_dihedral_angle_4_deg 16.941 r_dihedral_angle_3_deg 14.552 r_scangle_it 7.436 r_scbond_it 6.388 r_dihedral_angle_1_deg 6.314 r_mcangle_it 4.117 r_mcbond_it 3.068 r_angle_refined_deg 1.4 r_angle_other_deg 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.405 r_dihedral_angle_4_deg 16.941 r_dihedral_angle_3_deg 14.552 r_scangle_it 7.436 r_scbond_it 6.388 r_dihedral_angle_1_deg 6.314 r_mcangle_it 4.117 r_mcbond_it 3.068 r_angle_refined_deg 1.4 r_angle_other_deg 0.93 r_mcbond_other 0.45 r_symmetry_hbond_refined 0.211 r_symmetry_vdw_other 0.187 r_nbd_other 0.186 r_nbd_refined 0.185 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.149 r_symmetry_vdw_refined 0.126 r_nbtor_other 0.087 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5740 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction CCP4 data scaling