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Crystal structure of Retinoic Acid Receptor alpha (RXRA) in complexed with JP147
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LYQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 23% PEG 3350, 0.1 M Ammonium actetate, 0.1 M tris pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.07 40.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.648 α = 90 b = 65.648 β = 90 c = 110.816 γ = 90
Symmetry Space Group P 43 21 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 6M 2018-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.03320 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.9 46.42 99.9 0.037 0.042 0.015 1 20.7 7.8 19823
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 1.9 2 0.982 1.134 0.397 0.849 2 8.1
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 (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 1.9 42.85 18819 946 99.86 0.18187 0.17984 0.1889 0.2226 0.2283 RANDOM 53.195
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] 1.46 1.46 -2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.082 r_dihedral_angle_4_deg 21.382 r_dihedral_angle_3_deg 13.391 r_long_range_B_refined 7.814 r_long_range_B_other 7.811 r_dihedral_angle_1_deg 6.181 r_scangle_other 5.62 r_mcangle_it 4.338 r_mcangle_other 4.337 r_scbond_it 3.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.082 r_dihedral_angle_4_deg 21.382 r_dihedral_angle_3_deg 13.391 r_long_range_B_refined 7.814 r_long_range_B_other 7.811 r_dihedral_angle_1_deg 6.181 r_scangle_other 5.62 r_mcangle_it 4.338 r_mcangle_other 4.337 r_scbond_it 3.752 r_scbond_other 3.751 r_mcbond_it 2.969 r_mcbond_other 2.969 r_angle_refined_deg 1.368 r_angle_other_deg 1.336 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 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 1789 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing