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X-RAY DIFFRACTION
Materials and Methods page
4KRF
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 9
    Temperature 291.0
    Details 13% PEG 3350, 9% iso-propanol, 0.1M Tris pH 9.0, vapor diffusion, hanging drop, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 70.39 α = 90
    b = 97.73 β = 110.89
    c = 72.7 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 PSI PILATUS 6M
    Collection Date 2012-07-16
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 1.075
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.1
    Resolution(Low) 50
    Number Reflections(All) 50618
    Number Reflections(Observed) 50618
    Percent Possible(Observed) 94.2
    R Merge I(Observed) 0.041
    B(Isotropic) From Wilson Plot 40.298
     
    High Resolution Shell Details
    Resolution(High) 2.1
    Resolution(Low) 2.16
    Percent Possible(All) 64.1
    R Merge I(Observed) 0.32
    Mean I Over Sigma(Observed) 2.43
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.101
    Resolution(Low) 40.568
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 50614
    Number of Reflections(Observed) 50614
    Number of Reflections(R-Free) 2003
    Percent Reflections(Observed) 94.4
    R-Factor(Observed) 0.1772
    R-Work 0.1755
    R-Free 0.2173
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 38.0837
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.101
    Shell Resolution(Low) 2.1537
    Number of Reflections(R-Free) 92
    Number of Reflections(R-Work) 2364
    R-Factor(R-Work) 0.2395
    R-Factor(R-Free) 0.3294
    Percent Reflections(Observed) 64.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1537
    Shell Resolution(Low) 2.2119
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2816
    R-Factor(R-Work) 0.2111
    R-Factor(R-Free) 0.271
    Percent Reflections(Observed) 77.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2119
    Shell Resolution(Low) 2.277
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 3215
    R-Factor(R-Work) 0.2038
    R-Factor(R-Free) 0.2915
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.277
    Shell Resolution(Low) 2.3505
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3525
    R-Factor(R-Work) 0.1931
    R-Factor(R-Free) 0.2505
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3505
    Shell Resolution(Low) 2.4345
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 3641
    R-Factor(R-Work) 0.192
    R-Factor(R-Free) 0.2875
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4345
    Shell Resolution(Low) 2.5319
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3635
    R-Factor(R-Work) 0.1882
    R-Factor(R-Free) 0.2404
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5319
    Shell Resolution(Low) 2.6471
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 3655
    R-Factor(R-Work) 0.1842
    R-Factor(R-Free) 0.2559
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6471
    Shell Resolution(Low) 2.7867
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 3670
    R-Factor(R-Work) 0.19
    R-Factor(R-Free) 0.2234
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7867
    Shell Resolution(Low) 2.9612
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3662
    R-Factor(R-Work) 0.1889
    R-Factor(R-Free) 0.2392
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9612
    Shell Resolution(Low) 3.1898
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 3677
    R-Factor(R-Work) 0.184
    R-Factor(R-Free) 0.2187
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1898
    Shell Resolution(Low) 3.5106
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 3653
    R-Factor(R-Work) 0.1778
    R-Factor(R-Free) 0.2306
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5106
    Shell Resolution(Low) 4.0182
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 3662
    R-Factor(R-Work) 0.1595
    R-Factor(R-Free) 0.1809
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0182
    Shell Resolution(Low) 5.061
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 3705
    R-Factor(R-Work) 0.1481
    R-Factor(R-Free) 0.1649
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.061
    Shell Resolution(Low) 40.568
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 3731
    R-Factor(R-Work) 0.1722
    R-Factor(R-Free) 0.21
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 11.476
    f_plane_restr 0.003
    f_chiral_restr 0.048
    f_angle_d 0.723
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6580
    Nucleic Acid Atoms 259
    Heterogen Atoms 0
    Solvent Atoms 367
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction Xscale