POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4M94
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 6.5
    Temperature 293.15
    Details 7% PEG 4000, 5mM Magnesium acetate, 50mM N-(2-acetamido)iminodiacetic acid, pH 6.5, vapor diffusion, hanging drop, temperature 293.15K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 53.96 α = 90
    b = 145.72 β = 90
    c = 46.88 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type APEX II CCD
    Collection Date 2012-07-27
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SEALED TUBE
    Type OTHER
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.14
    Resolution(Low) 33.73
    Number Reflections(All) 21193
    Number Reflections(Observed) 19858
    Percent Possible(Observed) 93.7
    R Merge I(Observed) 0.047
    B(Isotropic) From Wilson Plot 19.05
    Redundancy 3.75
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.14
    Resolution(Low) 33.73
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 21193
    Number of Reflections(Observed) 19139
    Number of Reflections(R-Free) 398
    Percent Reflections(Observed) 90.6
    R-Factor(Observed) 0.202
    R-Work 0.201
    R-Free 0.239
     
    Temperature Factor Modeling
    Mean Isotropic B Value 29.54
    Anisotropic B[1][1] -1.5493
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -4.3218
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -6.8957
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.14
    Shell Resolution(Low) 2.4496
    Number of Reflections(R-Free) 103
    Number of Reflections(R-Work) 5189
    R-Factor(R-Work) 0.1973
    R-Factor(R-Free) 0.2397
    Percent Reflections(Observed) 77.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4496
    Shell Resolution(Low) 3.0859
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 6521
    R-Factor(R-Work) 0.1981
    R-Factor(R-Free) 0.2403
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0859
    Shell Resolution(Low) 33.7348
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 7031
    R-Factor(R-Work) 0.2017
    R-Factor(R-Free) 0.2367
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.065
    f_dihedral_angle_d 19.003
    f_angle_d 1.07
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2019
    Nucleic Acid Atoms 325
    Heterogen Atoms 16
    Solvent Atoms 148
     
     
  •   Software and Computing Hide
    Computing
    Data Collection APEX
    Data Reduction (intensity integration) SAINT
    Data Reduction (data scaling) XPREP
    Structure Solution PHASER
    Structure Refinement PHENIX (PHENIX.REFINE)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data collection SAINT