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Crystal structure of human retinoic X receptor alpha ligand-binding domain complexed with LX0278 and SRC1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P1T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 8% v/v Tacsimate pH8.0, 20% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.37 α = 90 b = 65.37 β = 90 c = 110.81 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 277 CCD MARMOSAIC 225 mm CCD 2010-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9753 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 31.36 16134
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2P1T 2 31.36 16134 96.01 0.20099 0.20099 25.441
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 r_dihedral_angle_2_deg 34.719 r_dihedral_angle_4_deg 20.335 r_dihedral_angle_3_deg 12.417 r_dihedral_angle_1_deg 4.32 r_scangle_it 1.742 r_angle_refined_deg 1.095 r_scbond_it 1.079 r_mcangle_it 0.787 r_mcbond_it 0.438 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.719 r_dihedral_angle_4_deg 20.335 r_dihedral_angle_3_deg 12.417 r_dihedral_angle_1_deg 4.32 r_scangle_it 1.742 r_angle_refined_deg 1.095 r_scbond_it 1.079 r_mcangle_it 0.787 r_mcbond_it 0.438 r_nbtor_refined 0.305 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.109 r_symmetry_hbond_refined 0.105 r_chiral_restr 0.072 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 1754 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 26
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling