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Vitamin D receptor complex with a carborane compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VJT PDB ENTRY 3VJT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1M MOPS/NaOH, 0.1-0.4M sodium formate, 12-22% PEG 4000, 5% ethylene glycol
, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.605 α = 90 b = 43.292 β = 95.28 c = 42.085 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 ADSC QUANTUM 4 2009-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.978 Photon Factory BL-6A
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 1.93 50 98.8 0.04 3.6 20819 20819 22.4
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-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3VJT 1.93 38.49 20819 1054 98.5 0.232 0.232 0.282 0.2663 RANDOM 43
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] -17.71 -3.69 24.95 -7.23
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.9 c_scangle_it 4.49 c_scbond_it 3.4 c_mcangle_it 2.78 c_mcbond_it 1.93 c_angle_deg 1.1 c_improper_angle_d 0.78 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.9 c_scangle_it 4.49 c_scbond_it 3.4 c_mcangle_it 2.78 c_mcbond_it 1.93 c_angle_deg 1.1 c_improper_angle_d 0.78 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2001 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 31
Software Software Software Name Purpose HKL-2000 data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing