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Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291.5 0.1M 3-(N-morpholino) propanesulfonic acid/sodium hydroxide, 0.1-0.4M sodium formate, 12-22% PEG 4000, 0-10% ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
Crystal Properties Matthews coefficient Solvent content 2.09 41.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.799 α = 90 b = 42.339 β = 96.38 c = 41.546 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 95 CCD ADSC QUANTUM 4r 2006-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.978 Photon Factory BL-6A
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 1.9 50 99.2 0.044 0.044 41.3 3.6 21020 24.2
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 1.9 1.96 99.8 0.329 0.329 4.7 3.5 1726
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 1.9 38.14 21789 19834 1955 93.4 0.234 0.2436 0.279 0.2854 RANDOM
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] -12.68 -6.36 17.09 -4.41
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.9 c_scangle_it 3.17 c_mcangle_it 2.53 c_scbond_it 2.16 c_mcbond_it 1.55 c_angle_deg 1.1 c_improper_angle_d 0.81 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2014 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 27
Software Software Software Name Purpose SERGUI data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing