POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3VFZ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.8
    Temperature 300.0
    Details 1.0-1.3M ammonium sulfate, 0.1M Tris-Cl, 5% 2-Methyl-2,4-pentanediol(MPD), 3% Glycerol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 300K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 80.43 α = 90
    b = 35.7 β = 122.59
    c = 50.92 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR scanner 300 mm plate
    Details Mirror
    Collection Date 2010-01-07
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE BM14
    Wavelength List 0.978
    Site ESRF
    Beamline BM14
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.9
    Resolution(Low) 33.88
    Number Reflections(Observed) 9711
    Percent Possible(Observed) 96.8
    R Merge I(Observed) 0.062
    Redundancy 7.1
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 2.0
    R Merge I(Observed) 0.588
    Mean I Over Sigma(Observed) 3.4
    Redundancy 7.1
    Number Unique Reflections(All) 10166
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 1.901
    Resolution(Low) 33.883
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 1.0
    Number of Reflections(Observed) 9478
    Number of Reflections(R-Free) 456
    Percent Reflections(Observed) 97.05
    R-Factor(Observed) 0.1999
    R-Work 0.1978
    R-Free 0.2384
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 46.9634
    Anisotropic B[1][1] -5.3144
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -3.8419
    Anisotropic B[2][2] 9.6949
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -4.3805
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9013
    Shell Resolution(Low) 2.1764
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2865
    R-Factor(R-Work) 0.2277
    R-Factor(R-Free) 0.2705
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1764
    Shell Resolution(Low) 2.7418
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 3046
    R-Factor(R-Work) 0.1855
    R-Factor(R-Free) 0.2685
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7418
    Shell Resolution(Low) 33.8884
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 3111
    R-Factor(R-Work) 0.197
    R-Factor(R-Free) 0.225
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.687
    f_plane_restr 0.003
    f_chiral_restr 0.059
    f_angle_d 0.9
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 943
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 13
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution SOLVE
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7_650)
    model building SOLVE
    data collection HKL-2000