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X-RAY DIFFRACTION
Materials and Methods page
3CLC
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 289.0
    Details 50 mM MES, 40 mM MgCl2, 25% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 104.48 α = 90
    b = 104.48 β = 90
    c = 139.29 γ = 120
     
    Space Group
    Space Group Name:    P 65
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2007-09-29
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID29
    Wavelength List 0.9322
    Site ESRF
    Beamline ID29
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.8
    Resolution(Low) 20
    Number Reflections(All) 21194
    Number Reflections(Observed) 21198
    Percent Possible(Observed) 98.5
    R Merge I(Observed) 0.043
    B(Isotropic) From Wilson Plot 63.204
     
    High Resolution Shell Details
    Resolution(High) 2.8
    Resolution(Low) 2.9
    Percent Possible(All) 98.5
    R Merge I(Observed) 0.393
    Mean I Over Sigma(Observed) 4.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.8
    Resolution(Low) 19.06
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 21157
    Number of Reflections(R-Free) 1086
    Percent Reflections(Observed) 99.81
    R-Factor(Observed) 0.209
    R-Work 0.207
    R-Free 0.239
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 94.261
    Anisotropic B[1][1] -0.23
    Anisotropic B[1][2] -0.11
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.23
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.34
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8
    Shell Resolution(Low) 2.871
    Number of Reflections(R-Free) 80
    Number of Reflections(R-Work) 1451
    R-Factor(R-Work) 0.365
    R-Factor(R-Free) 0.397
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.388
    r_scbond_it 2.159
    r_mcangle_it 1.689
    r_mcbond_it 1.117
    r_symmetry_hbond_refined 0.034
    r_bond_refined_d 0.007
    r_angle_refined_deg 1.328
    r_dihedral_angle_1_deg 8.556
    r_dihedral_angle_2_deg 38.065
    r_dihedral_angle_3_deg 24.805
    r_dihedral_angle_4_deg 17.41
    r_chiral_restr 0.093
    r_gen_planes_refined 0.011
    r_nbd_refined 0.295
    r_nbtor_refined 0.338
    r_xyhbond_nbd_refined 0.243
    r_symmetry_vdw_refined 0.341
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2496
    Nucleic Acid Atoms 1429
    Heterogen Atoms 2
    Solvent Atoms 4
     
     
  •   Software and Computing Hide
    Computing
    Data Collection XDS
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 3.004
    refinement REFMAC5
    molecular replacement Phaser
    data processing Xscale