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2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation and crystal structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RK3 PDB ENTRY 1RK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1-0.4 M formic acid, 15-20% polyethylene glycol(PEG)4000, 0-20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.859 α = 90 b = 41.998 β = 96.06 c = 41.951 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 95 CCD ADSC QUANTUM 4 2007-11-01 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 Merge 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 98.8 0.037 21 3.7 20949 17.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 99.9 0.162 8.7 3.6
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 1RK3 2 32.42 17326 1695 94.9 0.225 0.225 0.2247 0.261 0.2607 RANDOM 40
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] -16.44 -5.87 23.98 -7.54
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.6 c_scangle_it 5.42 c_scbond_it 4.29 c_mcangle_it 2.16 c_mcbond_it 1.42 c_angle_deg 0.9 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 19.6 c_scangle_it 5.42 c_scbond_it 4.29 c_mcangle_it 2.16 c_mcbond_it 1.42 c_angle_deg 0.9 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 2015 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 30
Software Software Software Name Purpose CNS refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing