POP-OUT | CLOSE

An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2FAK
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 293.0
    Details Crystals appeared after one week; Crystallization conditions: 40mg/ml yeast 20S proteasome 0.1M MES; 28mM MgAc2, 12% MPD 6h crystal soak with 10mM SalA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 135.17 α = 90
    b = 301.16 β = 112.82
    c = 144.14 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 MARRESEARCH
    Collection Date 2004-12-16
     
    Diffraction Radiation
    Monochromator SAGITALLY FOCUSED Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type MPG/DESY, HAMBURG BEAMLINE BW6
    Wavelength List 1.05
    Site MPG/DESY, HAMBURG
    Beamline BW6
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.8
    Resolution(Low) 15
    Number Reflections(All) 255532
    Number Reflections(Observed) 255532
    Percent Possible(Observed) 100.0
    B(Isotropic) From Wilson Plot 50.7
     
    High Resolution Shell Details
    Resolution(High) 2.82
    Resolution(Low) 2.87
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.467
    Number Unique Reflections(All) 271888
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 2.8
    Resolution(Low) 15.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 258110
    Number of Reflections(Observed) 242755
    Number of Reflections(R-Free) 12668
    Percent Reflections(Observed) 99.1
    R-Factor(All) 0.23
    R-Factor(Observed) 0.229
    R-Work 0.229
    R-Free 0.254
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 51.2
    Anisotropic B[1][1] 5.54
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -12.81
    Anisotropic B[2][2] -15.76
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 10.21
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8
    Shell Resolution(Low) 2.97
    Number of Reflections(R-Free) 2116
    Number of Reflections(R-Work) 40666
    R-Factor(R-Work) 0.352
    R-Factor(R-Free) 0.381
    R-Free Error 0.008
    Percent Reflections(Observed) 99.5
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 0.77
    c_dihedral_angle_d 23.2
    c_angle_deg 1.3
    c_bond_d 0.007
     
    Coordinate Error
    Luzzati ESD(Observed) 0.39
    Luzzati Sigma A(Observed) 0.54
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.44
    Luzzati Sigma A(R-Free Set) 0.59
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 49548
    Nucleic Acid Atoms 0
    Heterogen Atoms 120
    Solvent Atoms 1017
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution CNS
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1