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Crystal structure of an RNA duplex containing site specific 2'-amine substitution at a C-A mismatch (at pH 5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YRM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 273 MPD, Na cacodylate, spermine, calcium chloride, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.14 42.41
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 RAXIS IV++ 2003-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 2.5 23 98.6 0.08 0.1 11.65 14.29 4979 4904 1 60.4
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) 2.5 2.59 100 0.5 0.419 2.86 465
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 1YRM 2.55 8.08 4436 248 99.3 0.217 0.217 0.217 0.2366 0.262 0.2834 RANDOM 38.6
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] 7.13 2.72 7.13 -14.26
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 6.9 c_scangle_it 1.85 c_improper_angle_d 1.37 c_scbond_it 1.36 c_angle_deg 0.9 c_bond_d 0.005 c_mcbond_it c_mcangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1008 Solvent Atoms 34 Heterogen Atoms 1
Software Software Software Name Purpose CNS refinement CrystalClear data reduction SCALEPACK data scaling CNS phasing