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X-RAY DIFFRACTION
Materials and Methods page
4K4T
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    Temperature 289.0
    Details 0.16 M MgCl2, 0.08 M Tris-HCl, 24% (w/v) PEG 4000, 20% (v/v) glycerol and directly frozen for data collection , VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 59.4 α = 78.11
    b = 59.25 β = 78.09
    c = 97.46 γ = 78.85
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type NOIR-1
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 4.2.2
    Wavelength List 1.00
    Site ALS
    Beamline 4.2.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 1.5
    Resolution(High) 2.75
    Resolution(Low) 46.96
    Number Reflections(Observed) 31399
    Percent Possible(Observed) 96.1
    R Merge I(Observed) 0.069
    Redundancy 1.91
     
    High Resolution Shell Details
    Resolution(High) 2.75
    Resolution(Low) 2.85
    Percent Possible(All) 95.6
    R Merge I(Observed) 0.468
    Mean I Over Sigma(Observed) 1.8
    Redundancy 1.91
    Number Unique Reflections(All) 3149
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.75
    Resolution(Low) 46.959
    Cut-off Sigma(F) 1.96
    Number of Reflections(Observed) 31380
    Number of Reflections(R-Free) 1602
    Percent Reflections(Observed) 96.04
    R-Factor(Observed) 0.2047
    R-Work 0.2016
    R-Free 0.2623
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 67.9464
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.75
    Shell Resolution(Low) 2.8388
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2735
    R-Factor(R-Work) 0.3026
    R-Factor(R-Free) 0.3137
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8388
    Shell Resolution(Low) 2.9402
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 2671
    R-Factor(R-Work) 0.288
    R-Factor(R-Free) 0.3545
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9402
    Shell Resolution(Low) 3.0579
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.2806
    R-Factor(R-Free) 0.3358
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0579
    Shell Resolution(Low) 3.1971
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2717
    R-Factor(R-Work) 0.2625
    R-Factor(R-Free) 0.3541
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1971
    Shell Resolution(Low) 3.3656
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 2697
    R-Factor(R-Work) 0.2721
    R-Factor(R-Free) 0.3534
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3656
    Shell Resolution(Low) 3.5764
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2727
    R-Factor(R-Work) 0.2284
    R-Factor(R-Free) 0.2723
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5764
    Shell Resolution(Low) 3.8524
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2694
    R-Factor(R-Work) 0.204
    R-Factor(R-Free) 0.3121
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8524
    Shell Resolution(Low) 4.2398
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2745
    R-Factor(R-Work) 0.1753
    R-Factor(R-Free) 0.2311
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2398
    Shell Resolution(Low) 4.8528
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2712
    R-Factor(R-Work) 0.1588
    R-Factor(R-Free) 0.2107
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8528
    Shell Resolution(Low) 6.1119
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2699
    R-Factor(R-Work) 0.1832
    R-Factor(R-Free) 0.2281
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1119
    Shell Resolution(Low) 46.9656
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2697
    R-Factor(R-Work) 0.1792
    R-Factor(R-Free) 0.2294
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.6
    f_plane_restr 0.007
    f_chiral_restr 0.052
    f_angle_d 1.216
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7402
    Nucleic Acid Atoms 1418
    Heterogen Atoms 26
    Solvent Atoms 98
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BLU-ICE
    Data Reduction (intensity integration) d*TREK
    Data Reduction (data scaling) DTREK
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.8.2_1309)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction D*trek version: 9.9.9.1L