☰ Navigation Tabs
Crystal structure of rat VDR-LBD with 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 MOPS-Na, sodium formate, PEG 4000, ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.15 42.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.734 α = 90 b = 42.724 β = 95.55 c = 42.271 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 2007-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.97800 Photon Factory BL-6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 50 11212 29.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38
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 2ZLC 2.3 41.15 11212 1158 90.5 0.21 0.21 0.2096 0.245 0.2442 RANDOM 48.5
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] -21.51 -5.67 22.27 -0.76
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.7 c_scangle_it 7.65 c_scbond_it 6.61 c_mcangle_it 3.07 c_mcbond_it 1.95 c_angle_deg 0.6 c_improper_angle_d 0.59 c_bond_d 0.004 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.7 c_scangle_it 7.65 c_scbond_it 6.61 c_mcangle_it 3.07 c_mcbond_it 1.95 c_angle_deg 0.6 c_improper_angle_d 0.59 c_bond_d 0.004 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 2015 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 33
Software Software Software Name Purpose HKL-2000 data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing