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Crystal structure of LXRalpha in complex with tert-butyl benzoate analog, compound 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 PEG2000MME, ammonium sulfate, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.49 50.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.356 α = 90 b = 124.356 β = 90 c = 91.916 γ = 90
Symmetry Space Group P 4 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 IMAGE PLATE RIGAKU RAXIS IV 2003-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 2.7 40 99.5 0.084 14.6 15.2 20300
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 2.7 2.8 99.5 0.303 1982
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 1DB1 2.7 20 18276 2013 99.46 0.24695 0.24388 0.2444 0.27398 0.2752 RANDOM 40.538
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] 0.17 0.17 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.546 r_dihedral_angle_3_deg 17.124 r_dihedral_angle_4_deg 15.889 r_dihedral_angle_1_deg 5.463 r_angle_refined_deg 1.667 r_chiral_restr 0.095 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.546 r_dihedral_angle_3_deg 17.124 r_dihedral_angle_4_deg 15.889 r_dihedral_angle_1_deg 5.463 r_angle_refined_deg 1.667 r_chiral_restr 0.095 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 3965 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement DENZO data collection SCALEPACK data scaling CNS phasing PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data reduction