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Crystal structure of RXRalpha ligand-binding domain complexed with corepressor SMRT2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NSP PDB ENTRY 3NSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 100 mM sodium cacodylate, 15% PEG4000, 100 mM magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.57 52.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.22 α = 90 b = 118.22 β = 90 c = 84.02 γ = 90
Symmetry Space Group P 41 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 277 CCD MARMOSAIC 225 mm CCD 2011-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U SSRF BL17U
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 2.9 118.225 99.5 0.092 49.2 7.5 13739 13640 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 100 0.447 7.3 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 3NSP 2.9 44.77 12568 12568 651 100 0.24425 0.24004 0.2533 0.32626 0.2779 RANDOM 63.103
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] -0.05 -0.05 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.332 r_dihedral_angle_3_deg 23.137 r_dihedral_angle_4_deg 19.544 r_dihedral_angle_1_deg 7.725 r_scangle_it 2.813 r_angle_refined_deg 1.814 r_scbond_it 1.707 r_mcangle_it 1.32 r_mcbond_it 0.736 r_symmetry_hbond_refined 0.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.332 r_dihedral_angle_3_deg 23.137 r_dihedral_angle_4_deg 19.544 r_dihedral_angle_1_deg 7.725 r_scangle_it 2.813 r_angle_refined_deg 1.814 r_scbond_it 1.707 r_mcangle_it 1.32 r_mcbond_it 0.736 r_symmetry_hbond_refined 0.491 r_nbtor_refined 0.332 r_symmetry_vdw_refined 0.315 r_nbd_refined 0.293 r_xyhbond_nbd_refined 0.195 r_chiral_restr 0.117 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3556 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling