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Crystal structure of 16 base pair RNA duplex containing a C-A mismatch
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YRM pdb entry 1YRM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 273 MPD, sodium cacodylate, spermine, strontium chloride, magnesium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.14 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43 α = 90 b = 43 β = 90 c = 122 γ = 120
Symmetry Space Group P 31 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 IMAGE PLATE RIGAKU 2004-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 27 93.8 0.083 0.108 22.11 12.02 9573 8972 1 26.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 68.7 0.176 0.158 4.59 638
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 (All) 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 1YRM 2.1 19.01 7927 448 97.2 0.275 0.261 0.261 0.2563 0.28 0.2717 RANDOM 33.4
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] 4.87 3.33 4.87 -9.73
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 6.3 c_scangle_it 2.03 c_scbond_it 1.59 c_improper_angle_d 1.34 c_angle_deg 0.9 c_bond_d 0.004 c_mcbond_it c_mcangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1008 Solvent Atoms 67 Heterogen Atoms 2
Software Software Software Name Purpose CNS refinement CrystalClear data reduction SCALEPACK data scaling CNS phasing