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An Information Portal to 105906 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1PYX
  •   Crystallization Hide
    Crystallization Experiments
    pH 7
    Temperature 298.0
    Details PEG 3350 monodisperse, Glycerol, Magnesium Chloride, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.00
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 82.69 α = 90
    b = 85.21 β = 90
    c = 178.14 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
    Collection Date 2001-11-06
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-2
    Wavelength 0.933
    Site ESRF
    Beamline ID14-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.4
    Resolution(Low) 19.9
    Number Reflections(Observed) 49993
    Percent Possible(Observed) 98.9
    B(Isotropic) From Wilson Plot 32.8
    Redundancy 4.1
     
    High Resolution Shell Details
    Resolution(High) 2.4
    Resolution(Low) 2.49
    Percent Possible(All) 100.0
    Mean I Over Sigma(Observed) 3.1
    R-Sym I(Observed) 0.518
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.4
    Resolution(Low) 19.92
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 49502
    Number of Reflections(R-Free) 2468
    Percent Reflections(Observed) 99.1
    R-Work 0.206
    R-Free 0.233
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 43.1
    Anisotropic B[1][1] 5.53
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 7.04
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -12.57
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4
    Shell Resolution(Low) 2.55
    Number of Reflections(R-Free) 395
    Number of Reflections(R-Work) 7823
    R-Factor(R-Work) 0.262
    R-Factor(R-Free) 0.29
    R-Free Error 0.015
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 3.17
    c_scbond_it 2.09
    c_mcangle_it 2.42
    c_mcbond_it 1.41
    c_improper_angle_d 1.18
    c_bond_d 0.01
    c_angle_deg 1.5
    c_dihedral_angle_d 23.2
     
    Coordinate Error
    Luzzati ESD(Observed) 0.28
    Luzzati Sigma A(Observed) 0.27
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.32
    Luzzati Sigma A(R-Free Set) 0.33
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5449
    Nucleic Acid Atoms 0
    Heterogen Atoms 66
    Solvent Atoms 167
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (data scaling) SCALEPACK
    Structure Refinement CNX 2002 (ACCELRYS)
     
    Software
    refinement CNX version: 2002