POP-OUT | CLOSE

An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4NKU
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.1
    Temperature 291.0
    Details 0.1 M imidazole/MES, pH 6.1, 20% glycerol, 10% PEG4000, 126 mM halogens (sodium iodide, sodium bromide, sodium fluoride), 10 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 54.02 α = 90
    b = 77.09 β = 90.71
    c = 81.83 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 315r
    Collection Date 2012-06-04
     
    Diffraction Radiation
    Monochromator channel cut Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-4
    Wavelength List 0.9394
    Site ESRF
    Beamline ID14-4
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.94
    Resolution(Low) 45.34
    Number Reflections(All) 49786
    Number Reflections(Observed) 49569
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.093
    Redundancy 5.0
     
    High Resolution Shell Details
    Resolution(High) 1.94
    Percent Possible(All) 99.2
    R Merge I(Observed) 0.086
    Mean I Over Sigma(Observed) 2.28
    Redundancy 5.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.94
    Resolution(Low) 45.337
    Cut-off Sigma(F) 2.0
    Number of Reflections(all) 49786
    Number of Reflections(Observed) 49569
    Number of Reflections(R-Free) 2001
    Percent Reflections(Observed) 99.54
    R-Factor(Observed) 0.181
    R-Work 0.1792
    R-Free 0.2257
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.94
    Shell Resolution(Low) 1.9884
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 3359
    R-Factor(R-Work) 0.2175
    R-Factor(R-Free) 0.272
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9884
    Shell Resolution(Low) 2.0422
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3396
    R-Factor(R-Work) 0.2079
    R-Factor(R-Free) 0.2323
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0422
    Shell Resolution(Low) 2.1023
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 3348
    R-Factor(R-Work) 0.1985
    R-Factor(R-Free) 0.2799
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1023
    Shell Resolution(Low) 2.1701
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 3359
    R-Factor(R-Work) 0.1963
    R-Factor(R-Free) 0.2709
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1701
    Shell Resolution(Low) 2.2477
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 3422
    R-Factor(R-Work) 0.1972
    R-Factor(R-Free) 0.2723
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2477
    Shell Resolution(Low) 2.3377
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 3392
    R-Factor(R-Work) 0.1881
    R-Factor(R-Free) 0.2605
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3377
    Shell Resolution(Low) 2.4441
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 3371
    R-Factor(R-Work) 0.1854
    R-Factor(R-Free) 0.2603
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4441
    Shell Resolution(Low) 2.5729
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 3424
    R-Factor(R-Work) 0.1847
    R-Factor(R-Free) 0.2512
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5729
    Shell Resolution(Low) 2.7341
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3376
    R-Factor(R-Work) 0.1947
    R-Factor(R-Free) 0.2747
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7341
    Shell Resolution(Low) 2.9452
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 3395
    R-Factor(R-Work) 0.1899
    R-Factor(R-Free) 0.229
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9452
    Shell Resolution(Low) 3.2415
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 3418
    R-Factor(R-Work) 0.1839
    R-Factor(R-Free) 0.2227
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2415
    Shell Resolution(Low) 3.7103
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3414
    R-Factor(R-Work) 0.1619
    R-Factor(R-Free) 0.204
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7103
    Shell Resolution(Low) 4.6739
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 3439
    R-Factor(R-Work) 0.1494
    R-Factor(R-Free) 0.1689
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6739
    Shell Resolution(Low) 45.3497
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 3455
    R-Factor(R-Work) 0.1816
    R-Factor(R-Free) 0.2185
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.078
    f_dihedral_angle_d 15.364
    f_angle_d 1.077
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5111
    Nucleic Acid Atoms 78
    Heterogen Atoms 6
    Solvent Atoms 356
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) XDS package
    Data Reduction (data scaling) XDS package
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.1_1168)
    model building PHASER
    data collection ADSC version: Quantum