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Crystal Structure of TR3 LBD in complex with para-positioned 3,4,5-trisubstituted benzene derivatives
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 PEG4000, Sodium citrate, Glycerol
Crystal Properties Matthews coefficient Solvent content 3.36 63.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.844 α = 90 b = 76.441 β = 90 c = 129.417 γ = 90
Symmetry Space Group P 21 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 2018-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 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 2.6 50 99.9 0.889 19.769 6.3 23602
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 2.6 2.64 0.883
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.6 33.633 23602 1168 99.624 0.203 0.2006 0.2031 0.2426 0.2465 39.022
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] 0.194 0.054 -0.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.277 r_dihedral_angle_3_deg 19.463 r_dihedral_angle_4_deg 18.286 r_lrange_other 9.294 r_lrange_it 9.292 r_dihedral_angle_1_deg 6.126 r_scangle_it 5.924 r_scangle_other 5.922 r_mcangle_it 4.876 r_mcangle_other 4.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.277 r_dihedral_angle_3_deg 19.463 r_dihedral_angle_4_deg 18.286 r_lrange_other 9.294 r_lrange_it 9.292 r_dihedral_angle_1_deg 6.126 r_scangle_it 5.924 r_scangle_other 5.922 r_mcangle_it 4.876 r_mcangle_other 4.876 r_scbond_it 3.706 r_scbond_other 3.705 r_mcbond_it 3.17 r_mcbond_other 3.165 r_angle_refined_deg 1.563 r_angle_other_deg 1.244 r_nbd_refined 0.213 r_nbd_other 0.191 r_symmetry_nbd_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.184 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.164 r_xyhbond_nbd_other 0.12 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3584 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing