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Octameric RNA duplex co-crystallized with cobalt(II)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 6 293.15 25% MPD, 0.02 M magnesium sulfate, 0.0005 M spermine, 0.05 M potassium cacodylate pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.24 45.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.977 α = 90 b = 46.977 β = 90 c = 53.3 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 1.61 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 1.701 32.34 96.75 0.03729 55.81 15.7 4678
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 1.701 1.76 84.68 0.09058 12.1 4.1
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 1.701 32.339 2.2 4677 471 96.71 0.168 0.1646 0.1669 0.1976 0.1982
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 5.2 f_angle_d 0.401 f_chiral_restr 0.02 f_bond_d 0.019 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 334 Solvent Atoms 87 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing