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Development of Novel Lithocholic Acid Derivatives as Vitamin D Receptor Agonists
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1M MOPS/NaOH (pH 7.0), 0.1-0.4 M sodium formate, 12-22% (w/v) PEG4000, and 5%
(v/v) ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.17 43.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.884 α = 90 b = 43.69 β = 96.05 c = 41.792 γ = 90
Symmetry Space Group C 1 2 1
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 4r 2009-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.97800 Photon Factory BL-6A
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 1.8 50 98.6 0.043 16.3 3.5 25497
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 91.9 0.76 0.796 1.28 2.9
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 2ZLC 1.8 35.01 24273 1214 98.37 0.21324 0.21116 0.2215 0.25672 0.2664 RANDOM 41.527
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] -4.19 -0.97 6.32 -1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.564 r_dihedral_angle_4_deg 18.033 r_dihedral_angle_3_deg 15.91 r_long_range_B_other 6.396 r_long_range_B_refined 6.391 r_dihedral_angle_1_deg 5.68 r_scangle_other 5.473 r_mcangle_other 4.175 r_mcangle_it 4.173 r_scbond_it 3.596
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.564 r_dihedral_angle_4_deg 18.033 r_dihedral_angle_3_deg 15.91 r_long_range_B_other 6.396 r_long_range_B_refined 6.391 r_dihedral_angle_1_deg 5.68 r_scangle_other 5.473 r_mcangle_other 4.175 r_mcangle_it 4.173 r_scbond_it 3.596 r_scbond_other 3.595 r_mcbond_it 2.957 r_mcbond_other 2.94 r_angle_refined_deg 1.406 r_angle_other_deg 0.928 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 1984 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing