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Alternatingly modified 2'Fluoro RNA octamer f/rA2U2-P3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P4A PDB ENTRY 3P4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 Sodium cacodylate (40 mM, pH 6.0), sodium chloride (80 mM), barium chloride (20 mM), spermine tetrahydrochloride (12 mM), and 2-methyl-2,4-pentanediol (MPD; 10% (v/v)), equilibrated against a reservoir of MPD (1 mL, 35%), VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.18 43.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.383 α = 90 b = 43.383 β = 90 c = 60.987 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 CCD MARMOSAIC 225 mm CCD 2008-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.45 50 98.5 0.07 39 5.2 22793 21294
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) 1.45 1.48 81.8 0.42 1.34 2.6 1005
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 PDB ENTRY 3P4A 1.45 21.69 22442 21294 1141 100 0.19962 0.1971 0.2147 0.25083 0.2681 RANDOM 18.807
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] 0.8 0.4 0.8 -1.2
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.966 r_scbond_it 4.153 r_rigid_bond_restr 3.503 r_angle_refined_deg 2.077 r_chiral_restr 0.115 r_bond_refined_d 0.021 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1002 Solvent Atoms 141 Heterogen Atoms 2
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing