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Crystal structure of JMJD2A complexed with histone H3 peptide monomethylated at Lys9
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, 100 mM Citrate, 2 mM NiCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 48.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.209 α = 90 b = 149.842 β = 90 c = 57.47 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 CCD ADSC QUANTUM 315 2007-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0723 ESRF ID23-1
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 2.135 83.92 99.1 0.072 11.9 2.9 48784 48784 38
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 2.135 2.25 100 0.541 2 3 7095
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 2.135 20 45914 45914 2031 97.2 0.18909 0.18909 0.18676 0.1942 0.24072 0.2456 RANDOM 32.416
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] -0.97 0.04 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.971 r_dihedral_angle_3_deg 14.422 r_dihedral_angle_4_deg 14.22 r_dihedral_angle_1_deg 6.566 r_scangle_it 6.362 r_scbond_it 5.165 r_mcangle_it 3.331 r_mcbond_it 2.384 r_angle_refined_deg 1.33 r_angle_other_deg 0.897
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.971 r_dihedral_angle_3_deg 14.422 r_dihedral_angle_4_deg 14.22 r_dihedral_angle_1_deg 6.566 r_scangle_it 6.362 r_scbond_it 5.165 r_mcangle_it 3.331 r_mcbond_it 2.384 r_angle_refined_deg 1.33 r_angle_other_deg 0.897 r_mcbond_other 0.632 r_symmetry_vdw_other 0.252 r_symmetry_hbond_refined 0.232 r_symmetry_vdw_refined 0.198 r_nbd_refined 0.196 r_nbd_other 0.183 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.157 r_nbtor_other 0.085 r_chiral_restr 0.077 r_metal_ion_refined 0.039 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 5730 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement DNA data collection MOSFLM data reduction CCP4 data scaling