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Crystal structure of RXRalpha ligand binding domain in complex with triphenyltin and a coactivator fragment
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 7.5 293 PEG 4000, acetate ammonium, Tris-HCl, pH 7.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.635 α = 90 b = 64.635 β = 90 c = 113.589 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 CCD ADSC QUANTUM 210 2008-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 35 99.7 0.069 0.075 17.8 6.8 11258 11258
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 99.9 0.364 0.398 5.9 6.2
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 2P1T 2.3 28.09 11210 10771 439 99.56 0.18574 0.1834 0.1804 0.24437 0.2437 RANDOM 32.717
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 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.719 r_dihedral_angle_4_deg 22.208 r_dihedral_angle_3_deg 14.741 r_dihedral_angle_1_deg 5.122 r_scangle_it 2.495 r_scbond_it 1.625 r_angle_refined_deg 1.202 r_mcangle_it 1.039 r_mcbond_it 0.554 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.719 r_dihedral_angle_4_deg 22.208 r_dihedral_angle_3_deg 14.741 r_dihedral_angle_1_deg 5.122 r_scangle_it 2.495 r_scbond_it 1.625 r_angle_refined_deg 1.202 r_mcangle_it 1.039 r_mcbond_it 0.554 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1747 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 23
Software Software Software Name Purpose ADSC data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing