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An Information Portal to 111749 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1PXO
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.8
    Temperature 277.0
    Details PEG 6000, NA-HEPES, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 53.49 α = 90
    b = 71.99 β = 90
    c = 72.36 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
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SRS BEAMLINE PX14.1
    Wavelength List 1.488
    Site SRS
    Beamline PX14.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.96
    Resolution(Low) 15
    Number Reflections(Observed) 20604
    Percent Possible(Observed) 99.4
    R Merge I(Observed) 0.059
    B(Isotropic) From Wilson Plot 13.6
    Redundancy 10.97
     
    High Resolution Shell Details
    Resolution(High) 1.96
    Resolution(Low) 2.07
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.165
    Mean I Over Sigma(Observed) 7.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.96
    Resolution(Low) 14.99
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 20574
    Number of Reflections(R-Free) 1045
    Percent Reflections(Observed) 98.9
    R-Factor(All) 0.22
    R-Factor(Observed) 0.217
    R-Work 0.217
    R-Free 0.235
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 32.1
    Anisotropic B[1][1] -1.54
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -5.8
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 7.34
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.96
    Shell Resolution(Low) 2.07
    Number of Reflections(Observed) 3044
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3044
    R-Factor(R-Work) 0.252
    R-Factor(R-Free) 0.262
    R-Free Error 0.022
    Percent Reflections(Observed) 93.3
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 3.59
    c_scbond_it 2.36
    c_mcangle_it 3.25
    c_mcbond_it 1.9
    c_improper_angle_d 1.16
    c_bond_d 0.006
    c_angle_deg 1.3
    c_dihedral_angle_d 22.0
     
    Coordinate Error
    Luzzati ESD(Observed) 0.23
    Luzzati Sigma A(Observed) 0.16
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.25
    Luzzati Sigma A(R-Free Set) 0.18
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2366
    Nucleic Acid Atoms 0
    Heterogen Atoms 23
    Solvent Atoms 168
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MOLREP
    Structure Refinement CNS 1.0
     
    Software
    refinement CNS version: 1.0