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Crystal structure of the Jumonji domain of human Jumonji domain containing 1C protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 13% PEG3350, 200 MM SODIUM MALONATE
Crystal Properties Matthews coefficient Solvent content 2.26 45.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.718 α = 90 b = 112.206 β = 90 c = 165.173 γ = 90
Symmetry Space Group P 2 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 100 PIXEL DECTRIS PILATUS 6M 2012-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 2.1 92.82 100 0.15 11.5 15.6 50717 1.7
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 2.1 2.16 100 1.04 1.7 5.3
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 SAD THROUGHOUT NONE 2.1 92.82 48077 2574 99.97 0.21616 0.2149 0.2203 0.23986 0.2435 RANDOM 32.643
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] -2.49 -0.68 3.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.879 r_dihedral_angle_3_deg 14.244 r_dihedral_angle_4_deg 11.167 r_dihedral_angle_1_deg 6.137 r_angle_refined_deg 1.241 r_angle_other_deg 0.837 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.879 r_dihedral_angle_3_deg 14.244 r_dihedral_angle_4_deg 11.167 r_dihedral_angle_1_deg 6.137 r_angle_refined_deg 1.241 r_angle_other_deg 0.837 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5133 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling autoSHARP phasing