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Crystal structure of a mutant (P393GX) Thyroid Receptor Alpha ligand binding domain designed to model dominant negative human mutations.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2 M Sodium Chloride, 0.1 M Tris pH 8.5, 1.0 M Lithium Sulphate
Crystal Properties Matthews coefficient Solvent content 2.35 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.328 α = 90 b = 143.328 β = 90 c = 88.502 γ = 120
Symmetry Space Group P 64 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 PILATUS3 6M 2015-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9690 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 72.06 100 0.135 0.139 0.034 0.999 22 16.5 11208
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.18 100 0.7 0.721 0.17 0.948 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 MOLECULAR REPLACEMENT THROUGHOUT 2h79 3 72.06 11208 581 99.86 0.18555 0.18322 0.1868 0.22754 0.2302 RANDOM 52.545
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] -2.26 -1.13 -2.26 7.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.475 r_dihedral_angle_4_deg 21.251 r_dihedral_angle_3_deg 17.853 r_long_range_B_other 9.604 r_long_range_B_refined 9.603 r_scangle_other 7.948 r_dihedral_angle_1_deg 7.194 r_mcangle_it 6.394 r_mcangle_other 6.393 r_scbond_it 5.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.475 r_dihedral_angle_4_deg 21.251 r_dihedral_angle_3_deg 17.853 r_long_range_B_other 9.604 r_long_range_B_refined 9.603 r_scangle_other 7.948 r_dihedral_angle_1_deg 7.194 r_mcangle_it 6.394 r_mcangle_other 6.393 r_scbond_it 5.276 r_scbond_other 5.273 r_mcbond_it 4.324 r_mcbond_other 4.295 r_angle_refined_deg 2.059 r_angle_other_deg 0.977 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1854 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing