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Crystal structure of the Retinoid X Receptor alpha in complex with synthetic honokiol derivative 4 and a fragment of the TIF2 co-activator.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EC9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 0.1M PIPES, pH 7.0, 0.1M NaCl, 22% PEG 2K MME
Crystal Properties Matthews coefficient Solvent content 2.62 53.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.65 α = 90 b = 77.65 β = 90 c = 81.241 γ = 120
Symmetry Space Group P 32 2 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 PILATUS 200K 2016-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-003 1.541870
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 1.78 25.42 99.6 0.122 0.13 0.044 0.997 13.1 8.6 27516 13.62
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 1.78 1.82 94.1 0.685 0.842 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5EC9 1.78 25.417 1.34 27456 1319 99.49 0.1494 0.148 0.1522 0.1772 0.1831 17.6694
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.644 f_angle_d 1.358 f_chiral_restr 0.23 f_bond_d 0.018 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1739 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 39
Software Software Software Name Purpose Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction iMOSFLM data reduction