☰ Navigation Tabs
Crystal structure of the human VDR ligand binding domain bound to the natural metabolite 1alpha,25-dihydroxy-3-epi-vitamin D3
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, SITTING DROP 6 277 10mM Tris, 100mM NaCl, 1mM TCEP, 0.05M Mes, 0.7M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.54 51.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.889 α = 90 b = 51.12 β = 90 c = 132.196 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315r 2008-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.975531 ESRF ID29
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 48 94.3 0.078 0.078 11.3 2.5 24544 23145 15.1
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) 1.9 2 92.4 0.24 0.24 3.5 2.4 3268
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DB1 1.9 30 23481 21954 1169 93.46 0.17385 0.17231 0.174 0.20307 0.2044 RANDOM 15.42
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] -0.09 0.51 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.79 r_dihedral_angle_3_deg 11.832 r_dihedral_angle_4_deg 7.502 r_dihedral_angle_1_deg 4.284 r_scangle_it 2.027 r_scbond_it 1.292 r_angle_refined_deg 1.13 r_mcangle_it 0.858 r_mcbond_it 0.502 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.79 r_dihedral_angle_3_deg 11.832 r_dihedral_angle_4_deg 7.502 r_dihedral_angle_1_deg 4.284 r_scangle_it 2.027 r_scbond_it 1.292 r_angle_refined_deg 1.13 r_mcangle_it 0.858 r_mcbond_it 0.502 r_nbtor_refined 0.301 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.157 r_symmetry_hbond_refined 0.129 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2026 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 40
Software Software Software Name Purpose MxCuBE data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing