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Crystal Structure Analysis of the RNA Dodecamer CGC-(NF2)-AAUUAGCG, with an Incorporated 2,4-Difluorotoluyl Residue (NF2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Model of native A-RNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 Final droplet composition: 0.5 mM oligonucleotide, 5% MPD, 20 mM sodium cacodylate, pH 5.5, 10 mM cobalt hexamine, 20 mM LiCl and 10 mM MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.95 36.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.614 α = 90 b = 28.614 β = 90 c = 63.171 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 120 CCD MARRESEARCH 2004-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.992 APS 5ID-B
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 1.61 24.8 0.978 0.054 7538 7538
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) 1.61 1.66 0.969 0.53
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 (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 Model of native A-RNA 1.61 24.78 7538 7425 558 98.55 0.199 0.199 0.196 0.2043 0.231 0.2081 RANDOM 27.11
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] 1.03 0.52 1.03 -1.55
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.042 r_scbond_it 4.323 r_angle_refined_deg 2.066 r_angle_other_deg 1.504 r_xyhbond_nbd_other 0.422 r_xyhbond_nbd_refined 0.356 r_symmetry_hbond_refined 0.311 r_nbd_other 0.281 r_nbtor_refined 0.251 r_nbd_refined 0.182
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.042 r_scbond_it 4.323 r_angle_refined_deg 2.066 r_angle_other_deg 1.504 r_xyhbond_nbd_other 0.422 r_xyhbond_nbd_refined 0.356 r_symmetry_hbond_refined 0.311 r_nbd_other 0.281 r_nbtor_refined 0.251 r_nbd_refined 0.182 r_symmetry_vdw_other 0.177 r_nbtor_other 0.131 r_chiral_restr 0.092 r_symmetry_vdw_refined 0.086 r_gen_planes_refined 0.019 r_bond_refined_d 0.012 r_bond_other_d 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 506 Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement X-GEN data reduction X-GEN data scaling EPMR phasing