☰ Navigation Tabs
Human LXR-beta in complex with a ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 281 22% PEG 3350, 0.1 M Tris HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.17 43.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.137 α = 90 b = 106.888 β = 90 c = 150.803 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS PILATUS3 S 6M 2018-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9791 SSRF BL19U1
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 2.6 50.14 100 0.083 17.8 9.8 34182
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 0.296 2.6
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-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 5HJP 2.6 50.01 32375 1696 99.77 0.2635 0.2624 0.2619 0.28478 0.283 RANDOM 72.436
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] -3.02 4.77 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.05 r_dihedral_angle_3_deg 18.619 r_dihedral_angle_4_deg 17.124 r_long_range_B_other 7.405 r_long_range_B_refined 7.404 r_dihedral_angle_1_deg 5.135 r_mcangle_it 2.147 r_mcangle_other 2.146 r_scangle_other 1.417 r_mcbond_it 1.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.05 r_dihedral_angle_3_deg 18.619 r_dihedral_angle_4_deg 17.124 r_long_range_B_other 7.405 r_long_range_B_refined 7.404 r_dihedral_angle_1_deg 5.135 r_mcangle_it 2.147 r_mcangle_other 2.146 r_scangle_other 1.417 r_mcbond_it 1.145 r_mcbond_other 1.145 r_angle_refined_deg 1.122 r_angle_other_deg 0.932 r_scbond_it 0.73 r_scbond_other 0.73 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7522 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing