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Crystal structure of vitamin D receptor ligand binding domain complexed with a 19-norvitamin D compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZL9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 MOPS, Sodium Formate, PEG4000, Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 1.85 33.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.437 α = 90 b = 37.29 β = 98.47 c = 41.121 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 315 2014-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 50 99.7 0.128 0.151 0.08 7.3 3.5 12259
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 99.8 0.679 0.806 0.43 0.74 3.4 596
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2ZL9 2.3 50 9962 1039 92.8 0.2015 0.2018 0.2571 0.2572 Random 37.7062
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] -17.414 -1.723 4.863 12.552
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.044 c_mcangle_it 2.242 c_scbond_it 2.091 c_mcbond_it 1.373
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2009 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 37
Software Software Software Name Purpose HKL-2000 data scaling CNS refinement PDB_EXTRACT data extraction HKL-2000 data reduction CNS phasing