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Crystal structure of the Human TR4 DNA-Binding Domain 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 291 PEG4000, sodium citrate, ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.82 56.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.874 α = 90 b = 51.874 β = 90 c = 241.506 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 2019-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 SSRF BL17U
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 3.199 50 90.1 0.984 9.2 5.8 5486
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 3.199 3.28 0.95
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3DZU 3.199 47.708 5207 269 86.209 0.215 0.213 0.2154 0.2493 0.2787 53.473
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] -0.038 -0.038 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.514 r_dihedral_angle_3_deg 18.182 r_dihedral_angle_4_deg 12.609 r_lrange_other 9.074 r_lrange_it 9.072 r_dihedral_angle_1_deg 7.995 r_mcangle_other 7.273 r_mcangle_it 7.272 r_scangle_it 6.786 r_scangle_other 6.786
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.514 r_dihedral_angle_3_deg 18.182 r_dihedral_angle_4_deg 12.609 r_lrange_other 9.074 r_lrange_it 9.072 r_dihedral_angle_1_deg 7.995 r_mcangle_other 7.273 r_mcangle_it 7.272 r_scangle_it 6.786 r_scangle_other 6.786 r_mcbond_it 4.724 r_mcbond_other 4.705 r_scbond_it 4.492 r_scbond_other 4.482 r_angle_refined_deg 1.548 r_angle_other_deg 1.54 r_symmetry_xyhbond_nbd_refined 0.302 r_nbd_other 0.294 r_symmetry_nbd_other 0.217 r_nbtor_refined 0.204 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.161 r_xyhbond_nbd_other 0.13 r_symmetry_nbd_refined 0.127 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.028 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1024 Nucleic Acid Atoms 726 Solvent Atoms 59 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing