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Crystal structure of the Human TR4 Ligand Binding Domain in complex with the JAZF1 corepressor fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P0U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 HEPES, ammonium sulfate, sodium acetate, MPD
Crystal Properties Matthews coefficient Solvent content 2.28 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.851 α = 90 b = 76.851 β = 90 c = 98.365 γ = 90
Symmetry Space Group P 43 2 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 2021-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9793 SSRF BL02U1
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 1.856 50 98 0.998 36 9.5 25132
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 1.856 1.9 0.996
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 3P0U 1.856 28.09 24001 1248 93.747 0.198 0.1965 0.2064 0.2187 0.2269 19.405
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] -0.002 -0.002 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.434 r_dihedral_angle_4_deg 18.073 r_dihedral_angle_3_deg 15.117 r_dihedral_angle_1_deg 5.947 r_lrange_it 5.799 r_lrange_other 5.662 r_scangle_it 4.204 r_scangle_other 4.203 r_mcangle_it 3.184 r_mcangle_other 3.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.434 r_dihedral_angle_4_deg 18.073 r_dihedral_angle_3_deg 15.117 r_dihedral_angle_1_deg 5.947 r_lrange_it 5.799 r_lrange_other 5.662 r_scangle_it 4.204 r_scangle_other 4.203 r_mcangle_it 3.184 r_mcangle_other 3.183 r_scbond_it 2.724 r_scbond_other 2.721 r_mcbond_it 2.035 r_mcbond_other 2.034 r_angle_refined_deg 1.583 r_angle_other_deg 1.429 r_symmetry_nbd_refined 0.356 r_nbd_other 0.242 r_symmetry_xyhbond_nbd_refined 0.219 r_nbd_refined 0.207 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.132 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1886 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing