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X-RAY DIFFRACTION
Materials and Methods page
3UFD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 289.0
    Details 0.1 M SPG buffer, 25% w/v PEG 1500, 10 uM Spermidine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 47.49 α = 90
    b = 147.1 β = 93.68
    c = 47.78 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2009-11-11
     
    Diffraction Radiation
    Monochromator Double crystal, Si(111) or Si(311)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-4
    Wavelength List 0.9395
    Site ESRF
    Beamline ID14-4
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.7
    Resolution(Low) 73.55
    Number Reflections(All) 17783
    Number Reflections(Observed) 17783
    Percent Possible(Observed) 98.9
    Redundancy 3.4
     
    High Resolution Shell Details
    Resolution(High) 2.7
    Resolution(Low) 2.85
    Percent Possible(All) 99.7
    R Merge I(Observed) 0.201
    Mean I Over Sigma(Observed) 3.8
    R-Sym I(Observed) 0.201
    Redundancy 3.5
    Number Unique Reflections(All) 2610
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.8
    Resolution(Low) 45.36
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 22705
    Number of Reflections(Observed) 15885
    Number of Reflections(R-Free) 791
    Percent Reflections(Observed) 98.71
    R-Factor(Observed) 0.2072
    R-Work 0.2057
    R-Free 0.2367
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 50.88
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.01
    Anisotropic B[2][2] -0.14
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.13
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8
    Shell Resolution(Low) 2.873
    Number of Reflections(R-Free) 42
    Number of Reflections(R-Work) 1106
    R-Factor(R-Work) 0.265
    R-Factor(R-Free) 0.355
    Percent Reflections(Observed) 99.83
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.897
    r_scbond_it 1.146
    r_mcangle_it 0.719
    r_mcbond_it 0.359
    r_gen_planes_refined 0.005
    r_chiral_restr 0.067
    r_dihedral_angle_4_deg 25.046
    r_dihedral_angle_3_deg 16.973
    r_dihedral_angle_2_deg 28.486
    r_dihedral_angle_1_deg 4.714
    r_angle_refined_deg 1.52
    r_bond_refined_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2479
    Nucleic Acid Atoms 1546
    Heterogen Atoms 1
    Solvent Atoms 13
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MXCUBE
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0110
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    molecular replacement Phaser version: 2.1.4
    data reduction SCALA version: 3.3.9
    data collection Mosflm