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Crystal Structure of Vitamin D Receptor and 9-cis Retinoic Acid Receptor DNA-Binding Domains Bound to a DR3 Response Element
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KB4 PDB ENTRY 1KB4 and 1DSZ experimental model PDB 1DSZ PDB ENTRY 1KB4 and 1DSZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 PEG 8000, ammonium citrate, Tris, glycerol, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.2 70.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.104 α = 90 b = 57.049 β = 110.31 c = 73.438 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 MARRESEARCH 2002-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.1808 APS 14-ID-B
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 3 50 96.3 0.045 31.2 3.4 18127 -3
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 3 3.11 97.5 0.34 2.6 1844
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1KB4 and 1DSZ 3 50 8849 823 87.6 0.232 0.2336 0.283 0.2899 RANDOM 97.6
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] -20.69 -18.54 24.55 -3.86
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.5 c_scangle_it 2.65 c_scbond_it 1.63 c_mcangle_it 1.61 c_angle_deg 1.6 c_improper_angle_d 1.42 c_mcbond_it 0.91 c_bond_d 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1335 Nucleic Acid Atoms 731 Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data reduction CNS refinement HKL-2000 data scaling CNS phasing