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crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MbisP and a synthetic peptide containing 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 VAPOR DIFFUSION, HANGING DROP 7 295 PEG 4000, MOPS, ammonium citrate, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.05 39.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.447 α = 90 b = 44.114 β = 96.62 c = 41.86 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 2003-01-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
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 1.9 42.4 99 0.032 20.8 4.8 22362 22171 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) 1.9 1.99 90 0.153 3.4
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 (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 1RJK 1.9 30 22161 22161 1133 99.21 0.19442 0.19442 0.19266 0.1946 0.22631 RANDOM 30.886
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] -2.48 -0.38 2.72 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.121 r_scangle_it 4.511 r_scbond_it 2.779 r_mcangle_it 1.734 r_angle_refined_deg 1.378 r_mcbond_it 0.917 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.121 r_scangle_it 4.511 r_scbond_it 2.779 r_mcangle_it 1.734 r_angle_refined_deg 1.378 r_mcbond_it 0.917 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.093 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2006 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement SAINT data reduction LSCALE data scaling