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An Information Portal to 110790 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1YM2
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.5
    Temperature 292.0
    Details Ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 82.26 α = 90
    b = 103.26 β = 104.12
    c = 100.62 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Collection Date 2004-01-28
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06SA
    Wavelength List 1.00033
    Site SLS
    Beamline X06SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.05
    Resolution(Low) 100
    Number Reflections(All) 102160
    Number Reflections(Observed) 102160
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.047
    B(Isotropic) From Wilson Plot 33.3
    Redundancy 6.4
     
    High Resolution Shell Details
    Resolution(High) 2.05
    Resolution(Low) 2.12
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.485
    Redundancy 6.2
    Number Unique Reflections(All) 9710
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.05
    Resolution(Low) 47.05
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 102108
    Number of Reflections(Observed) 102108
    Number of Reflections(R-Free) 10253
    Percent Reflections(Observed) 99.7
    R-Factor(All) 0.215
    R-Factor(Observed) 0.215
    R-Work 0.212
    R-Free 0.237
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 48.4
    Anisotropic B[1][1] 5.02
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -2.66
    Anisotropic B[2][2] -1.63
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -3.39
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.05
    Shell Resolution(Low) 2.18
    Number of Reflections(Observed) 16904
    Number of Reflections(R-Free) 1728
    Number of Reflections(R-Work) 15176
    R-Factor(R-Work) 0.278
    R-Factor(R-Free) 0.304
    R-Free Error 0.007
    Percent Reflections(Observed) 99.8
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 2.86
    c_scbond_it 1.93
    c_mcangle_it 2.39
    c_mcbond_it 1.47
    c_improper_angle_d 0.68
    c_dihedral_angle_d 25.1
    c_angle_deg 1.2
    c_bond_d 0.004
     
    Coordinate Error
    Luzzati ESD(Observed) 0.27
    Luzzati Sigma A(Observed) 0.2
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.3
    Luzzati Sigma A(R-Free Set) 0.24
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9027
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 578
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution CNX 2002
    Structure Refinement CNX 2002
     
    Software
    refinement CNX version: 2002