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An Information Portal to 110790 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4AGZ
  •   Crystallization Hide
    Crystallization Experiments
    pH 6.5
    Details MAGNESIUM CHLORIDE, DNA, DB 985, MPD, SODIUM CACODYLATE BUFFER. PH 6.6, VAPOUR DIFFUSION, SITTING DROP, 285K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 24.03 α = 90
    b = 39.9 β = 90
    c = 65.78 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
    Details TOROIDAL MIRROR
    Collection Date 2009-07-19
     
    Diffraction Radiation
    Monochromator SI (111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-4
    Wavelength 0.9765
    Site ESRF
    Beamline ID14-4
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.25
    Resolution(Low) 39.9
    Number Reflections(Observed) 18006
    Percent Possible(Observed) 99.0
    R Merge I(Observed) 0.05
    B(Isotropic) From Wilson Plot 0.0
    Redundancy 6.5
     
    High Resolution Shell Details
    Resolution(High) 1.25
    Resolution(Low) 1.32
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.55
    Mean I Over Sigma(Observed) 3.1
    Redundancy 6.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.25
    Resolution(Low) 14.76
    Number of Reflections(Observed) 17027
    Number of Reflections(R-Free) 925
    Percent Reflections(Observed) 98.84
    R-Factor(Observed) 0.15755
    R-Work 0.15483
    R-Free 0.20704
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 12.92
    Anisotropic B[1][1] -0.12
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.12
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.25
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.25
    Shell Resolution(Low) 1.282
    Number of Reflections(R-Free) 82
    Number of Reflections(R-Work) 1230
    R-Factor(R-Work) 0.212
    R-Factor(R-Free) 0.274
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 7.302
    r_rigid_bond_restr 2.644
    r_scangle_it 4.309
    r_scbond_it 3.329
    r_gen_planes_other 0.037
    r_gen_planes_refined 0.034
    r_chiral_restr 0.111
    r_angle_other_deg 4.559
    r_angle_refined_deg 2.574
    r_bond_other_d 0.001
    r_bond_refined_d 0.02
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 0
    Nucleic Acid Atoms 486
    Heterogen Atoms 31
    Solvent Atoms 192
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0110
     
    Software
    refinement REFMAC version: 5.5.0110
    model building PHASER