POP-OUT | CLOSE

An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3E7X
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Temperature 293.0
    Details 30% PEG 1000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 45.76 α = 90
    b = 91.39 β = 90
    c = 121.47 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 180
     
    Diffraction Detector
    Detector CCD
    Type MAR CCD 165 mm
    Details mirrors
    Collection Date 2005-04-01
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type BESSY BEAMLINE 14.1
    Wavelength List 0.91438
    Site BESSY
    Beamline 14.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.6
    Resolution(Low) 30
    Number Reflections(All) 16387
    Number Reflections(Observed) 15976
    Percent Possible(Observed) 97.5
    R Merge I(Observed) 0.047
    B(Isotropic) From Wilson Plot 34.719
    Redundancy 3.01
     
    High Resolution Shell Details
    Resolution(High) 2.6
    Resolution(Low) 2.68
    Percent Possible(All) 98.9
    R Merge I(Observed) 0.218
    Mean I Over Sigma(Observed) 5.3
    R-Sym I(Observed) 0.269
    Redundancy 2.89
    Number Unique Reflections(All) 1406
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.6
    Resolution(Low) 19.92
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 16387
    Number of Reflections(Observed) 15932
    Number of Reflections(R-Free) 1037
    Percent Reflections(Observed) 97.8
    R-Work 0.179
    R-Free 0.238
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model GROUP
    Mean Isotropic B Value 39.412
    Anisotropic B[1][1] -1.18
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -3.63
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 4.81
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6
    Shell Resolution(Low) 2.64
    Number of Reflections(Observed) 818
    Number of Reflections(R-Free) 53
    Number of Reflections(R-Work) 755
    R-Factor(R-Work) 0.255
    R-Factor(R-Free) 0.328
    R-Free Error 0.045
    Percent Reflections(Observed) 98.3
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 0.84
    c_dihedral_angle_d 23.5
    c_angle_deg 1.3
    c_bond_d 0.006
     
    Coordinate Error
    Luzzati ESD(Observed) 0.26
    Luzzati Sigma A(Observed) 0.43
    Luzzati Resolution Cutoff(Low) 3.0
    Luzzati ESD(R-Free Set) 0.38
    Luzzati Sigma A(R-Free Set) 0.54
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3978
    Nucleic Acid Atoms 0
    Heterogen Atoms 23
    Solvent Atoms 211
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) XSCALE
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement CNS 1.1
     
    Software
    data extraction pdb_extract version: 3.006
    refinement CNS
    molecular replacement Phaser
    data processing Xscale