☰ Navigation Tabs
Crystal structure of JMJ2D2A in ternary complex with histone H3-K36me2 and succinate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GP5
Crystallization Crystal Properties Matthews coefficient Solvent content 2.61 52.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.857 α = 90 b = 148.642 β = 90 c = 57.346 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 200 CCD MARMOSAIC 300 mm CCD 2007-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.00 APS 23-ID-D
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 2.29 37.8 0.09 0.073 36.1 4.7 38447 2 1
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) 2.29 2.38 0.471 0.452 2.7 3 1099
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 2GP5 2.29 37.8 1 2 38402 1927 97 0.20602 0.20362 0.2397 0.25057 0.2784 RANDOM 36.28
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] -0.32 -0.35 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.968 r_dihedral_angle_4_deg 19.5 r_dihedral_angle_3_deg 17.724 r_dihedral_angle_1_deg 5.825 r_scangle_it 2.16 r_scbond_it 1.408 r_angle_refined_deg 1.294 r_mcangle_it 0.943 r_mcbond_it 0.539 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.968 r_dihedral_angle_4_deg 19.5 r_dihedral_angle_3_deg 17.724 r_dihedral_angle_1_deg 5.825 r_scangle_it 2.16 r_scbond_it 1.408 r_angle_refined_deg 1.294 r_mcangle_it 0.943 r_mcbond_it 0.539 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.252 r_symmetry_vdw_refined 0.2 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5672 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing