POP-OUT | CLOSE

An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4F4Y
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.1
    Temperature 298.0
    Details 10% PEG-3350, 100 mM Ca(OAc)2, 100 mM HEPES, 2.5% Glycerol, 250mM sucrose, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 53.08 α = 90
    b = 103.39 β = 101.76
    c = 112.99 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 ADSC QUANTUM 315
    Collection Date 2011-10-07
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 1.1
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.34
    Resolution(Low) 30
    Number Reflections(All) 49979
    Number Reflections(Observed) 47630
    Percent Possible(Observed) 95.3
    R Merge I(Observed) 0.084
    Redundancy 2.8
     
    High Resolution Shell Details
    Resolution(High) 2.35
    Resolution(Low) 2.39
    Percent Possible(All) 80.7
    R Merge I(Observed) 0.245
    Mean I Over Sigma(Observed) 3.9
    Redundancy 1.7
    Number Unique Reflections(All) 2002
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.338
    Resolution(Low) 29.25
    Cut-off Sigma(F) 1.53
    Number of Reflections(Observed) 47570
    Number of Reflections(R-Free) 1890
    Percent Reflections(Observed) 94.1
    R-Factor(Observed) 0.2234
    R-Work 0.2219
    R-Free 0.2586
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -9.1291
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 5.8228
    Anisotropic B[2][2] -8.0482
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 17.1773
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3382
    Shell Resolution(Low) 2.4014
    Number of Reflections(R-Free) 110
    Number of Reflections(R-Work) 2597
    R-Factor(R-Work) 0.2998
    R-Factor(R-Free) 0.3612
    Percent Reflections(Observed) 70.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4014
    Shell Resolution(Low) 2.472
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 3299
    R-Factor(R-Work) 0.3229
    R-Factor(R-Free) 0.3813
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.472
    Shell Resolution(Low) 2.5517
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 3430
    R-Factor(R-Work) 0.2971
    R-Factor(R-Free) 0.3752
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5517
    Shell Resolution(Low) 2.6429
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 3520
    R-Factor(R-Work) 0.3011
    R-Factor(R-Free) 0.3234
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6429
    Shell Resolution(Low) 2.7486
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 3470
    R-Factor(R-Work) 0.29
    R-Factor(R-Free) 0.3476
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7486
    Shell Resolution(Low) 2.8736
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 3558
    R-Factor(R-Work) 0.2878
    R-Factor(R-Free) 0.3796
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8736
    Shell Resolution(Low) 3.025
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 3609
    R-Factor(R-Work) 0.2464
    R-Factor(R-Free) 0.3364
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.025
    Shell Resolution(Low) 3.2143
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 3665
    R-Factor(R-Work) 0.2212
    R-Factor(R-Free) 0.2535
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2143
    Shell Resolution(Low) 3.4621
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 3661
    R-Factor(R-Work) 0.2136
    R-Factor(R-Free) 0.2561
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4621
    Shell Resolution(Low) 3.8098
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 3702
    R-Factor(R-Work) 0.2115
    R-Factor(R-Free) 0.2503
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8098
    Shell Resolution(Low) 4.3596
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 3682
    R-Factor(R-Work) 0.1794
    R-Factor(R-Free) 0.2095
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3596
    Shell Resolution(Low) 5.4867
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 3719
    R-Factor(R-Work) 0.1819
    R-Factor(R-Free) 0.2156
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4867
    Shell Resolution(Low) 29.2519
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3768
    R-Factor(R-Work) 0.2005
    R-Factor(R-Free) 0.1829
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.063
    f_dihedral_angle_d 19.075
    f_angle_d 1.11
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5460
    Nucleic Acid Atoms 1378
    Heterogen Atoms 52
    Solvent Atoms 252
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER in PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.3_928)
    model building PHASER version: in PHENIX
    data collection CBASS