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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DSK
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Details 0.2 M calcium acetate, 0.1 M sodium cacodylate (pH 6.5), 18% v/v PEG8000, VAPOR DIFFUSION, SITTING DROP
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 86.69 α = 90
    b = 93.34 β = 90
    c = 106.36 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
    Details mirrors
    Collection Date 2011-06-27
     
    Diffraction Radiation
    Monochromator mirror
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X12B
    Wavelength List 1.0000
    Site NSLS
    Beamline X12B
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.18
    Resolution(Low) 70.16
    Number Reflections(All) 45712
    Number Reflections(Observed) 44295
    Percent Possible(Observed) 96.9
    Redundancy 5.6
     
    High Resolution Shell Details
    Resolution(High) 2.18
    Resolution(Low) 2.26
    Percent Possible(All) 78.5
    Mean I Over Sigma(Observed) 2.2
    R-Sym I(Observed) 0.374
    Redundancy 2.3
    Number Unique Reflections(All) 4497
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.18
    Resolution(Low) 70.16
    Number of Reflections(all) 45712
    Number of Reflections(Observed) 39669
    Number of Reflections(R-Free) 4433
    Percent Reflections(Observed) 96.48
    R-Factor(All) 0.1909
    R-Factor(Observed) 0.1909
    R-Work 0.18509
    R-Free 0.24275
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 32.076
    Anisotropic B[1][1] 1.87
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.11
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.77
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.18
    Shell Resolution(Low) 2.236
    Number of Reflections(R-Free) 273
    Number of Reflections(R-Work) 2237
    R-Factor(R-Work) 0.273
    R-Factor(R-Free) 0.334
    Percent Reflections(Observed) 75.63
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.807
    r_scbond_it 2.988
    r_mcangle_it 1.767
    r_mcbond_it 0.896
    r_gen_planes_refined 0.008
    r_chiral_restr 0.114
    r_dihedral_angle_4_deg 18.785
    r_dihedral_angle_3_deg 17.744
    r_dihedral_angle_2_deg 38.03
    r_dihedral_angle_1_deg 5.919
    r_angle_refined_deg 1.758
    r_bond_refined_d 0.018
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4617
    Nucleic Acid Atoms 497
    Heterogen Atoms 13
    Solvent Atoms 300
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASES
    Structure Refinement REFMAC 5.5.0109
     
    Software
    refinement REFMAC version: 5.5.0109
    model building PHASES
    data collection HKL-2000