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Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20Z and the NR2 Box of DRIP 205
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RJK PDB ENTRY 1RJK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 macroseeding in batch 7 295 PEG 4000, MOPS, Ammonium Citrate, Isopropanol, pH 7.0, macroseeding in batch, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.98 38.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.5 α = 90 b = 42.4 β = 96.5 c = 41.9 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 BRUKER PROTEUM R Montel Optics 2005-11-30 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.74 42.5 99.8 0.0448 19.4 6.1 27636 27577 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.74 1.85 99.4 0.321 2.86 3.54 4160
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1RJK 1.74 30 26241 26241 1388 98.43 0.201 0.199 0.1982 0.246 0.2466 RANDOM 26.413
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] -2.5 -0.43 2.91 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.045 r_dihedral_angle_4_deg 19.253 r_dihedral_angle_3_deg 13.933 r_dihedral_angle_1_deg 5.027 r_scangle_it 3.866 r_scbond_it 2.507 r_mcangle_it 1.628 r_angle_refined_deg 1.56 r_mcbond_it 1.022 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.045 r_dihedral_angle_4_deg 19.253 r_dihedral_angle_3_deg 13.933 r_dihedral_angle_1_deg 5.027 r_scangle_it 3.866 r_scbond_it 2.507 r_mcangle_it 1.628 r_angle_refined_deg 1.56 r_mcbond_it 1.022 r_nbtor_refined 0.309 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.166 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2000 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction LSCALE data scaling