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Crystal structure of the agonist-bound ligand-binding domain of Biomphalaria glabrata RXR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FBY PDB ENTRY 1FBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 HEPES, sodium formate, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.17 61.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.1 α = 90 b = 87.1 β = 90 c = 320.4 γ = 120
Symmetry Space Group P 61 2 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 CCD ADSC QUANTUM 210 2003-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 25 0.094 19.5 15.6 25831 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.65 99.1 0.54 5.98 15.8
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 1FBY 2.5 24.4 24537 24538 1292 100 0.1958 0.19326 0.19 0.24332 0.2402 RANDOM 46.191
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] 2.07 1.03 2.07 -3.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.313 r_dihedral_angle_4_deg 27.667 r_dihedral_angle_3_deg 21.767 r_dihedral_angle_1_deg 7.149 r_scangle_it 5.974 r_scbond_it 3.824 r_angle_refined_deg 2.589 r_mcangle_it 2.31 r_mcbond_it 1.4 r_nbtor_refined 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.313 r_dihedral_angle_4_deg 27.667 r_dihedral_angle_3_deg 21.767 r_dihedral_angle_1_deg 7.149 r_scangle_it 5.974 r_scbond_it 3.824 r_angle_refined_deg 2.589 r_mcangle_it 2.31 r_mcbond_it 1.4 r_nbtor_refined 0.34 r_symmetry_vdw_refined 0.297 r_nbd_refined 0.267 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.162 r_symmetry_hbond_refined 0.147 r_bond_refined_d 0.029 r_gen_planes_refined 0.01 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 3691 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing