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Crystal structure of the Human TR4 DNA-Binding Domain with C-terminal extension (DBD-CTE) Homodimer Bound to DR1 Response Element
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DZU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 PEG 8000, Tris, ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.69 54.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.146 α = 90 b = 52.146 β = 90 c = 242.701 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS 2M 2021-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9793 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.297 50 96.3 0.998 20.2 7.1 15386
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.297 2.36 0.853
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3DZU 2.3 31.53 13569 683 85.2 0.188 0.1957 0.215 0.1964 31.95
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] -0.037 -0.037 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.265 r_dihedral_angle_4_deg 17.773 r_dihedral_angle_3_deg 15.901 r_dihedral_angle_1_deg 7.711 r_scangle_it 5.626 r_scangle_other 5.625 r_mcangle_other 5.081 r_mcangle_it 5.08 r_scbond_it 3.761 r_scbond_other 3.761
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.265 r_dihedral_angle_4_deg 17.773 r_dihedral_angle_3_deg 15.901 r_dihedral_angle_1_deg 7.711 r_scangle_it 5.626 r_scangle_other 5.625 r_mcangle_other 5.081 r_mcangle_it 5.08 r_scbond_it 3.761 r_scbond_other 3.761 r_mcbond_it 3.36 r_mcbond_other 3.351 r_angle_refined_deg 1.904 r_angle_other_deg 1.523 r_nbd_other 0.295 r_nbd_refined 0.197 r_nbtor_refined 0.197 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.085 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbtor_other 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_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 1226 Nucleic Acid Atoms 732 Solvent Atoms 264 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing