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crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MD 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 1DB1 PDB entry 1DB1
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 2.01 38.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.6 α = 90 b = 43.292 β = 96.07 c = 41.848 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 2002-10-27 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 1.99 33.07 99 0.051 10.8 4.9 19031 18940 3
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) 1.99 2.08 96 0.161 3.5
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1DB1 1.99 30 18937 18937 977 99.54 0.18814 0.18814 0.18502 0.1863 0.24433 RANDOM 30.927
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] -2.94 -0.48 3.45 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.895 r_scangle_it 4.184 r_scbond_it 2.573 r_mcangle_it 1.637 r_angle_refined_deg 1.394 r_mcbond_it 0.87 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.895 r_scangle_it 4.184 r_scbond_it 2.573 r_mcangle_it 1.637 r_angle_refined_deg 1.394 r_mcbond_it 0.87 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.089 r_symmetry_hbond_refined 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1990 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement SAINT data reduction LSCALE data scaling MOLREP phasing