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Octameric RNA duplex soaked in terbium(III)chloride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U3L PDB entry 4U3L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 28% PEG 400, 0.2 M calcium chloride, 0.002 M spermine, 0.05 M hepes sodium buffer pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.33 47.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.506 α = 90 b = 46.506 β = 90 c = 56.627 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 100 PIXEL DECTRIS PILATUS 2M 2013-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.64 SLS X06SA
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 1.952 32.82 96.82 0.04999 33.19 9.8 3225
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) 1 1.952 2.02 89.57 0.4356 5.35 9
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 4U3L 1.952 32.82 2.01 3224 329 96.76 0.1755 0.172 0.1733 0.2067 0.2055
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 5.437 f_angle_d 0.783 f_chiral_restr 0.026 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 334 Solvent Atoms 37 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing