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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1RI8
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.5
    Temperature 293.0
    Details PEG 4000, lithium sulphate, Tris-HCl, glycerol, sodium chloride, potassium phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 51.5 α = 90
    b = 53.43 β = 90
    c = 104.45 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 2002-03-11
     
    Diffraction Radiation
    Monochromator SAGITALLY FOCUSED Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-2
    Wavelength List 0.933
    Site ESRF
    Beamline ID14-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.85
    Resolution(Low) 30
    Number Reflections(All) 25306
    Number Reflections(Observed) 24895
    Percent Possible(Observed) 98.4
    R Merge I(Observed) 0.077
    B(Isotropic) From Wilson Plot 12.9
    Redundancy 5.9
     
    High Resolution Shell Details
    Resolution(High) 1.85
    Resolution(Low) 1.92
    Percent Possible(All) 91.4
    R Merge I(Observed) 0.25
    Mean I Over Sigma(Observed) 5.7
    R-Sym I(Observed) 0.25
    Redundancy 3.6
    Number Unique Reflections(All) 2178
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.85
    Resolution(Low) 29.17
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 25306
    Number of Reflections(Observed) 24895
    Number of Reflections(R-Free) 1254
    Percent Reflections(Observed) 98.3
    R-Factor(All) 0.174
    R-Factor(Observed) 0.174
    R-Work 0.173
    R-Free 0.196
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 17.2
    Anisotropic B[1][1] -1.21
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.9
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.31
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.85
    Shell Resolution(Low) 1.97
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3601
    R-Factor(R-Work) 0.202
    R-Factor(R-Free) 0.253
    R-Free Error 0.018
    Percent Reflections(Observed) 91.7
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 4.75
    c_scbond_it 3.6
    c_mcangle_it 2.96
    c_mcbond_it 2.33
    c_improper_angle_d 0.92
    c_dihedral_angle_d 25.2
    c_angle_deg 1.6
    c_bond_d 0.014
     
    Coordinate Error
    Luzzati ESD(Observed) 0.17
    Luzzati Sigma A(Observed) 0.06
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.19
    Luzzati Sigma A(R-Free Set) 0.14
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1886
    Nucleic Acid Atoms 0
    Heterogen Atoms 6
    Solvent Atoms 231
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) CCP4 (TRUNCATE)
    Structure Solution AMORE
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1