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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 2ZLC PDB ENTRY 2ZLC
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 2.14 42.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.855 α = 90 b = 42.319 β = 95.59 c = 42.176 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 2007-11-07 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 2 50 99.7 0.049 4.7 18571 18571 22.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2ZLC 2 40.81 18571 950 99.7 0.23 0.23 0.2219 0.266 0.254 RANDOM 44.1
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] -16.24 -7.35 16.74 -0.51
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.6 c_scangle_it 5.03 c_scbond_it 3.7 c_mcangle_it 2.97 c_mcbond_it 2.09 c_angle_deg 1.1 c_improper_angle_d 0.77 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.6 c_scangle_it 5.03 c_scbond_it 3.7 c_mcangle_it 2.97 c_mcbond_it 2.09 c_angle_deg 1.1 c_improper_angle_d 0.77 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 1992 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 31
Software Software Software Name Purpose HKL-2000 data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing