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RXRa structure complexed with CU-6PMN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 20% (w/v) Polyethylene glycol 3350, 0.2M Mg(OAc)2
Crystal Properties Matthews coefficient Solvent content 2.32 46.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.615 α = 90 b = 99.386 β = 99.42 c = 110.158 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 2018-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.65 46 99.7 0.134 10.7 6.7 27286 37.9
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 2.65 2.72 95.8 0.716 0.706
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 5GYM 2.65 46 27286 1425 99.65 0.22596 0.22345 0.2281 0.27442 0.2742 RANDOM 50.2
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] -0.03 0.01 0.05 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.906 r_dihedral_angle_4_deg 23.392 r_dihedral_angle_3_deg 19.783 r_long_range_B_refined 12.032 r_long_range_B_other 12.031 r_scangle_other 8.988 r_mcangle_it 7.953 r_mcangle_other 7.953 r_dihedral_angle_1_deg 7.49 r_scbond_it 5.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.906 r_dihedral_angle_4_deg 23.392 r_dihedral_angle_3_deg 19.783 r_long_range_B_refined 12.032 r_long_range_B_other 12.031 r_scangle_other 8.988 r_mcangle_it 7.953 r_mcangle_other 7.953 r_dihedral_angle_1_deg 7.49 r_scbond_it 5.871 r_scbond_other 5.871 r_mcbond_it 5.432 r_mcbond_other 5.426 r_angle_refined_deg 1.132 r_angle_other_deg 1.083 r_chiral_restr 0.046 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d r_gen_planes_other 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 6262 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing