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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1YM4
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.4
    Temperature 292.0
    Details PEG 8000, potassium chloride, 1,2-propanediol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 223.68 α = 90
    b = 107.75 β = 100.32
    c = 61.47 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 MARRESEARCH
    Collection Date 2002-12-19
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06SA
    Wavelength List 0.855064
    Site SLS
    Beamline X06SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.25
    Resolution(Low) 100
    Number Reflections(All) 68076
    Number Reflections(Observed) 68076
    Percent Possible(Observed) 98.5
    R Merge I(Observed) 0.083
    B(Isotropic) From Wilson Plot 41.0
    Redundancy 5.1
     
    High Resolution Shell Details
    Resolution(High) 2.25
    Resolution(Low) 2.33
    Percent Possible(All) 89.0
    R Merge I(Observed) 0.29
    Redundancy 4.4
    Number Unique Reflections(All) 6217
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.25
    Resolution(Low) 96.77
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 68076
    Number of Reflections(Observed) 67661
    Number of Reflections(R-Free) 6850
    Percent Reflections(Observed) 99.3
    R-Factor(All) 0.245
    R-Factor(Observed) 0.245
    R-Work 0.24
    R-Free 0.288
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 48.5
    Anisotropic B[1][1] -19.25
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -9.58
    Anisotropic B[2][2] -5.8
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 25.05
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.25
    Shell Resolution(Low) 2.39
    Number of Reflections(Observed) 11070
    Number of Reflections(R-Free) 1077
    Number of Reflections(R-Work) 9993
    R-Factor(R-Work) 0.403
    R-Factor(R-Free) 0.428
    R-Free Error 0.013
    Percent Reflections(Observed) 97.8
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 4.22
    c_scbond_it 3.01
    c_mcangle_it 3.52
    c_mcbond_it 2.23
    c_improper_angle_d 0.83
    c_dihedral_angle_d 25.6
    c_angle_deg 1.3
    c_bond_d 0.008
     
    Coordinate Error
    Luzzati ESD(Observed) 0.34
    Luzzati Sigma A(Observed) 0.53
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.43
    Luzzati Sigma A(R-Free Set) 0.58
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9051
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 487
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution CNX 2000.1
    Structure Refinement CNX 2002
     
    Software
    refinement CNX version: 2002