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RXRa structure complexed with CU-6PMN and SRC1 peptide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 30%(v/v) Polyethylene glycol monomethyl ether 550, 0.1M HEPES-NaOH (pH 7.5), 0.05M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.02 39.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.39 α = 90 b = 64.39 β = 90 c = 111.168 γ = 90
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 S 6M 2018-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00 Photon Factory BL-5A
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 2.3 64.4 99.8 0.11 0.996 24 13.6 19042 28
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 2.3 2.36 97.8 0.428 0.968
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 3OAP 2.3 64.39 19042 943 99.78 0.18139 0.17853 0.1856 0.238 0.2482 RANDOM 35.221
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 35.754 r_dihedral_angle_4_deg 22.862 r_dihedral_angle_3_deg 15.573 r_long_range_B_refined 8.385 r_long_range_B_other 8.384 r_scangle_other 7.312 r_dihedral_angle_1_deg 6.76 r_scbond_it 5.318 r_scbond_other 5.317 r_mcangle_it 5.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.754 r_dihedral_angle_4_deg 22.862 r_dihedral_angle_3_deg 15.573 r_long_range_B_refined 8.385 r_long_range_B_other 8.384 r_scangle_other 7.312 r_dihedral_angle_1_deg 6.76 r_scbond_it 5.318 r_scbond_other 5.317 r_mcangle_it 5.227 r_mcangle_other 5.226 r_mcbond_it 3.877 r_mcbond_other 3.877 r_angle_refined_deg 2.344 r_angle_other_deg 1.192 r_chiral_restr 0.137 r_gen_planes_refined 0.013 r_bond_refined_d 0.008 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 3558 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing