☰ Navigation Tabs
Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 0.1M Citrate, 4mM NiCl2, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.4 48.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.21 α = 90 b = 150.004 β = 90 c = 57.228 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 MARMOSAIC 225 mm CCD 2007-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.91820 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.95 41.49 99.6 0.072 0.084 12 3.6 64355 64097 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 98.4 0.589 0.699 2 3.3 9121
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 1.95 41.49 61370 61370 2679 99.49 0.17047 0.17047 0.16871 0.1748 0.20999 0.2126 RANDOM 29.491
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] -0.8 -0.12 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.61 r_dihedral_angle_4_deg 13.077 r_dihedral_angle_3_deg 12.843 r_dihedral_angle_1_deg 5.924 r_scangle_it 5.276 r_scbond_it 3.801 r_mcangle_it 2.584 r_mcbond_it 1.802 r_angle_refined_deg 1.139 r_angle_other_deg 0.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.61 r_dihedral_angle_4_deg 13.077 r_dihedral_angle_3_deg 12.843 r_dihedral_angle_1_deg 5.924 r_scangle_it 5.276 r_scbond_it 3.801 r_mcangle_it 2.584 r_mcbond_it 1.802 r_angle_refined_deg 1.139 r_angle_other_deg 0.857 r_mcbond_other 0.481 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.191 r_nbtor_refined 0.181 r_nbd_other 0.178 r_symmetry_vdw_other 0.165 r_xyhbond_nbd_refined 0.127 r_symmetry_vdw_refined 0.103 r_nbtor_other 0.087 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 5737 Nucleic Acid Atoms Solvent Atoms 483 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction CCP4 data scaling PHASER phasing