POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1PY5
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.6
    Temperature 298.0
    Details Tris, ATP, MgCl2, DTT, Hexanediol, PEG4000, LiSO4, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 41.83 α = 90
    b = 78.11 β = 90
    c = 90.69 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 200
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Details mirrors
    Collection Date 2000-06-10
     
    Diffraction Radiation
    Monochromator Yale Mirrors
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 17-ID
    Wavelength List 1.0
    Site APS
    Beamline 17-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 2.3
    Resolution(Low) 20
    Number Reflections(All) 13208
    Number Reflections(Observed) 13178
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.09
    B(Isotropic) From Wilson Plot 17.3
    Redundancy 6.0
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.44
    Percent Possible(All) 74.7
    R Merge I(Observed) 0.185
    Mean I Over Sigma(Observed) 5.0
    Redundancy 4.0
    Number Unique Reflections(All) 1607
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.3
    Resolution(Low) 20.0
    Cut-off Sigma(F) 1.0
    Number of Reflections(all) 13208
    Number of Reflections(Observed) 13178
    Number of Reflections(R-Free) 669
    R-Factor(All) 0.26
    R-Factor(Observed) 0.258
    R-Work 0.258
    R-Free 0.292
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 21.4
    Anisotropic B[1][1] 0.18
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 3.13
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -3.31
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.44
    Number of Reflections(Observed) 1607
    Number of Reflections(R-Free) 79
    R-Factor(R-Work) 0.267
    R-Factor(R-Free) 0.31
    R-Free Error 0.041
    Percent Reflections(Observed) 74.7
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_mcangle_it 2.5
    c_mcbond_it 1.51
    c_improper_angle_d 0.85
    c_dihedral_angle_d 22.6
    c_angle_deg 1.5
    c_bond_d 0.01
     
    Coordinate Error
    Luzzati ESD(Observed) 0.034
    Luzzati Sigma A(Observed) 0.2
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.039
    Luzzati Sigma A(R-Free Set) 0.38
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2418
    Nucleic Acid Atoms 0
    Heterogen Atoms 26
    Solvent Atoms 146
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution AMORE
    Structure Refinement CNS
     
    Software
    refinement CNS
    model building AMoRE
    data reduction SCALEPACK
    data collection HKL-2000