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Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m22G:A pairs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other canonical A-form RNA dodecamer omitting U13 and U26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 301 2ul droplets containing 0.5mM oligonucleotide, 5% 2-methyl -2,4-pentanediol (MPD), 20mM
sodium cacodylate, pH 7.0, 6mM spermine-4HCl, 40mM sodium chloride that were equilibrated against a reservoir of 1ml of 35% MPD., VAPOR DIFFUSION, HANGING DROP, temperature 301K
Crystal Properties Matthews coefficient Solvent content 2.02 39.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.118 α = 90 b = 25.97 β = 97.41 c = 45.393 γ = 90
Symmetry Space Group C 1 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 120 CCD MARMOSAIC 225 mm CCD 2004-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.00 APS 22-BM
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 1.8 44.99 93.9 0.099 26.4 2 6420 6027
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) 1.8 1.86 81.4 0.3539 4.8 1.9 661
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 A cononical A-RNA dodecamer generated with the program TURBO-FRODO omitting U13 and U26. 1.8 44.99 6420 4816 582 84.12 0.19938 0.19005 0.2171 0.27742 0.2885 RANDOM 25.807
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] -1.88 0.63 0.18 1.86
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.993 r_scbond_it 1.582 r_angle_refined_deg 1.356 r_angle_other_deg 1.124 r_nbd_other 0.249 r_nbtor_refined 0.236 r_symmetry_vdw_other 0.212 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.146 r_nbd_refined 0.108
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.993 r_scbond_it 1.582 r_angle_refined_deg 1.356 r_angle_other_deg 1.124 r_nbd_other 0.249 r_nbtor_refined 0.236 r_symmetry_vdw_other 0.212 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.146 r_nbd_refined 0.108 r_symmetry_vdw_refined 0.084 r_nbtor_other 0.077 r_xyhbond_nbd_other 0.075 r_chiral_restr 0.051 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 556 Solvent Atoms 115 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection X-GEN data reduction X-GEN data scaling MOLREP phasing