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Crystal structure of the human Liver X receptor beta ligand binding domain in complex with a synthetic agonist
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FCY PDB ENTRY 1FCY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 RESERVOIR: 25% MPD, 10% PEG4K, 100 MM HEPES PH 7.5, 10 MM D PROTEIN: 4-8 MG/ML IN 20 MM TRIS PH 8.0, 100 MM NACL, 10 MM
Crystal Properties Matthews coefficient Solvent content 2.6 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.22 α = 90 b = 43.276 β = 90 c = 51.615 γ = 90
Symmetry Space Group P 21 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 100 CCD MARRESEARCH MIRRORS 2002-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.4 89 89.9 0.121 4.7 2.8 11049
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 2.4 2.53 92.4 0.395 1.7 2.8
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-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1FCY 2.4 20 10504 527 87.6 0.25 0.295 RANDOM 13.18
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] 2.22 -1.87 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.461 r_scangle_it 3.243 r_scbond_it 1.873 r_angle_refined_deg 1.358 r_mcangle_it 1.129 r_mcbond_it 0.574 r_symmetry_vdw_refined 0.261 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.461 r_scangle_it 3.243 r_scbond_it 1.873 r_angle_refined_deg 1.358 r_mcangle_it 1.129 r_mcbond_it 0.574 r_symmetry_vdw_refined 0.261 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1875 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing