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Crystal structure of human RXRalpha ligand binding domain complexed with CBTF-EE.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZQU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 5% [v/v] tacsimateTM [pH 7.0], 0.1 M HEPES [pH 7.0], and 10% [w/v] PEGMME5000
Crystal Properties Matthews coefficient Solvent content 2.15 42.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.757 α = 90 b = 99.432 β = 98.31 c = 93.598 γ = 90
Symmetry Space Group P 1 21 1
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 2M 2018-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.15 47.14 95.6 0.081 0.996 16.2 6.5 48015
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 0.498 0.86 1.7
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 5ZQU 2.15 47.14 45567 2423 95.59 0.22283 0.22052 0.2239 0.26633 0.267 RANDOM 50.897
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.767 r_dihedral_angle_4_deg 22.007 r_dihedral_angle_3_deg 17.983 r_long_range_B_other 10.374 r_long_range_B_refined 10.373 r_scangle_other 7.997 r_mcangle_it 6.564 r_mcangle_other 6.564 r_dihedral_angle_1_deg 6.375 r_scbond_it 5.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.767 r_dihedral_angle_4_deg 22.007 r_dihedral_angle_3_deg 17.983 r_long_range_B_other 10.374 r_long_range_B_refined 10.373 r_scangle_other 7.997 r_mcangle_it 6.564 r_mcangle_other 6.564 r_dihedral_angle_1_deg 6.375 r_scbond_it 5.421 r_scbond_other 5.42 r_mcbond_it 4.743 r_mcbond_other 4.731 r_angle_refined_deg 2.001 r_angle_other_deg 1.314 r_chiral_restr 0.232 r_bond_refined_d 0.009 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 6268 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing