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Structure of a nonameric RNA duplex at room temperature in ChipX microfluidic device
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 485D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 6 300 RNA solution: 10 mg/mL in 10 mM Na-cacodylate pH 6.0, 5 mM MgCl2.
Reservoir solution: 2.6 M ammonium sulfate, 50 mM Na-cacodylate pH 6.0,
5 mM MgSO4, 1 mM spermine.
Crystallization and crystallographic analysis were performed using the ChipX microfluidic device.
Crystal Properties Matthews coefficient Solvent content 1.83 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40 α = 90 b = 40 β = 90 c = 69.11 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD MARMOSAIC 225 mm CCD 2011-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.55 24 91.5 0.157 0.179 0.988 6.1 3.9 5485 -3 23.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.59 69.7 0.367 0.455 0.755 1.8 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 485D 1.55 23.037 2.55 5484 382 91.52 0.2073 0.1924 0.1948 0.2228 0.2223 Random selection
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.74 f_angle_d 0.68 f_chiral_restr 0.031 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 342 Solvent Atoms 43 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing