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X-RAY DIFFRACTION
Materials and Methods page
1N7A
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 298.0
    Details 1 mM (single strand) RNA, 20 mM sodium cacodylate buffer, pH 6.0, 5 mM spermine tetrachloride, 32 mM KCl and 2 % (v/v) methyl-2,4-pentanediol (MPD) against 25 % MPD in the reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 31.23 α = 90
    b = 51.1 β = 90
    c = 70.65 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
    Collection Date 2002-02-08
     
    Diffraction Radiation
    Monochromator diamond(111) and Ge(200)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-2
    Wavelength List 0.933
    Site ESRF
    Beamline ID14-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.2
    Resolution(Low) 20
    Number Reflections(All) 35974
    Number Reflections(Observed) 35974
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.087
    B(Isotropic) From Wilson Plot 4.9
    Redundancy 4.24
     
    High Resolution Shell Details
    Resolution(High) 1.2
    Resolution(Low) 1.27
    Percent Possible(All) 98.5
    R Merge I(Observed) 0.341
    Mean I Over Sigma(Observed) 3.82
    Redundancy 4.19
    Number Unique Reflections(All) 5469
     
     
  •   Refinement Hide
    Refinement Statistics
    reflnsShellList 1.2
    Resolution(Low) 20.0
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 35974
    Number of Reflections(Observed) 35974
    Number of Reflections(R-Free) 1802
    Percent Reflections(Observed) 99.71
    R-Factor(All) 0.12533
    R-Factor(Observed) 0.12533
    R-Work 0.12369
    R-Free 0.15626
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model The DNA/RNA and K-atoms were refined anisotropically, the spermine and waters isotropic
    Mean Isotropic B Value 9.356
    Anisotropic B[1][1] 0.02
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.2
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.22
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.201
    Shell Resolution(Low) 1.265
    Number of Reflections(R-Free) 268
    Number of Reflections(R-Work) 4872
    R-Factor(R-Work) 0.167
    R-Factor(R-Free) 0.208
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 4.684
    r_bond_refined_d 0.01
    r_angle_refined_deg 1.533
    r_chiral_restr 0.072
    r_gen_planes_refined 0.019
    r_nbd_refined 0.374
    r_xyhbond_nbd_refined 0.081
    r_symmetry_vdw_refined 0.133
    r_symmetry_hbond_refined 0.144
    r_scbond_it 2.12
    r_scangle_it 2.79
    r_rigid_bond_restr 1.164
    r_sphericity_free 2.853
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 0
    Nucleic Acid Atoms 1024
    Heterogen Atoms 31
    Solvent Atoms 181
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) PRODC
    Data Reduction (data scaling) XDS
    Structure Solution SHELXD, SHARP
    Structure Refinement REFMAC 5.1.24
     
    Software
    refinement REFMAC version: 5.1.24
    model building sharp
    model building shelxd
    data reduction XDS
    data collection prodc