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X-RAY DIFFRACTION
Materials and Methods page
3NWD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.5
    Temperature 293.0
    Details 10% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 117.76 α = 90
    b = 117.76 β = 90
    c = 318.56 γ = 120
     
    Space Group
    Space Group Name:    P 3
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2008-08-26
     
    Diffraction Radiation
    Monochromator SAGITALLY FOCUSED Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 1.0809
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.88
    Resolution(Low) 48.56
    Number Reflections(All) 111822
    Number Reflections(Observed) 111383
    Percent Possible(Observed) 99.6074
    R Merge I(Observed) 0.132
    Redundancy 4.6
     
    High Resolution Shell Details
    Resolution(High) 2.88
    Resolution(Low) 2.98
    Percent Possible(All) 97.0
    Mean I Over Sigma(Observed) 1.04
    Redundancy 3.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.8803
    Resolution(Low) 48.5625
    Cut-off Sigma(F) 0.07
    Number of Reflections(all) 111822
    Number of Reflections(Observed) 98380
    Number of Reflections(R-Free) 4990
    Percent Reflections(Observed) 87.9791
    R-Factor(Observed) 0.2405
    R-Work 0.2381
    R-Free 0.2829
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 0.4117
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.4117
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.8233
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9684
    Shell Resolution(Low) 3.0157
    Number of Reflections(R-Free) 573
    Number of Reflections(R-Work) 3149
    R-Factor(R-Work) 0.3453
    R-Factor(R-Free) 0.3887
    Percent Reflections(Observed) 66.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0157
    Shell Resolution(Low) 3.0663
    Number of Reflections(R-Free) 23
    Number of Reflections(R-Work) 3702
    R-Factor(R-Work) 0.3284
    R-Factor(R-Free) 0.341
    Percent Reflections(Observed) 79.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0663
    Shell Resolution(Low) 3.1204
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 3914
    R-Factor(R-Work) 0.3336
    R-Factor(R-Free) 0.0
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1204
    Shell Resolution(Low) 3.1786
    Number of Reflections(R-Free) 431
    Number of Reflections(R-Work) 3654
    R-Factor(R-Work) 0.3013
    R-Factor(R-Free) 0.3548
    Percent Reflections(Observed) 76.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1786
    Shell Resolution(Low) 3.2414
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 3778
    R-Factor(R-Work) 0.3045
    R-Factor(R-Free) 0.367
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2414
    Shell Resolution(Low) 3.3094
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 4056
    R-Factor(R-Work) 0.2974
    R-Factor(R-Free) 0.0
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3094
    Shell Resolution(Low) 3.3835
    Number of Reflections(R-Free) 260
    Number of Reflections(R-Work) 4018
    R-Factor(R-Work) 0.286
    R-Factor(R-Free) 0.2631
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3835
    Shell Resolution(Low) 3.4648
    Number of Reflections(R-Free) 385
    Number of Reflections(R-Work) 3872
    R-Factor(R-Work) 0.2754
    R-Factor(R-Free) 0.2989
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4648
    Shell Resolution(Low) 3.5545
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 4253
    R-Factor(R-Work) 0.2723
    R-Factor(R-Free) 0.0
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5545
    Shell Resolution(Low) 3.6542
    Number of Reflections(R-Free) 60
    Number of Reflections(R-Work) 4201
    R-Factor(R-Work) 0.2735
    R-Factor(R-Free) 0.2853
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6542
    Shell Resolution(Low) 3.7662
    Number of Reflections(R-Free) 634
    Number of Reflections(R-Work) 3672
    R-Factor(R-Work) 0.2536
    R-Factor(R-Free) 0.3049
    Percent Reflections(Observed) 78.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7662
    Shell Resolution(Low) 3.8933
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 4396
    R-Factor(R-Work) 0.2413
    R-Factor(R-Free) 0.0
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8933
    Shell Resolution(Low) 4.0395
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 4332
    R-Factor(R-Work) 0.2318
    R-Factor(R-Free) 0.0
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0395
    Shell Resolution(Low) 4.2104
    Number of Reflections(R-Free) 710
    Number of Reflections(R-Work) 3730
    R-Factor(R-Work) 0.2234
    R-Factor(R-Free) 0.2832
    Percent Reflections(Observed) 78.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2104
    Shell Resolution(Low) 4.4146
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 4362
    R-Factor(R-Work) 0.201
    R-Factor(R-Free) 0.0
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4146
    Shell Resolution(Low) 4.6651
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 4424
    R-Factor(R-Work) 0.1835
    R-Factor(R-Free) 0.0
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6651
    Shell Resolution(Low) 4.9844
    Number of Reflections(R-Free) 698
    Number of Reflections(R-Work) 3705
    R-Factor(R-Work) 0.1885
    R-Factor(R-Free) 0.2409
    Percent Reflections(Observed) 78.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9844
    Shell Resolution(Low) 5.414
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 4424
    R-Factor(R-Work) 0.2013
    R-Factor(R-Free) 0.0
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.414
    Shell Resolution(Low) 6.0449
    Number of Reflections(R-Free) 0
    Number of Reflections(R-Work) 4435
    R-Factor(R-Work) 0.2269
    R-Factor(R-Free) 0.0
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0449
    Shell Resolution(Low) 7.1348
    Number of Reflections(R-Free) 711
    Number of Reflections(R-Work) 3725
    R-Factor(R-Work) 0.2336
    R-Factor(R-Free) 0.268
    Percent Reflections(Observed) 79.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.002
    f_chiral_restr 0.034
    f_dihedral_angle_d 12.201
    f_angle_d 0.493
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19175
    Nucleic Acid Atoms 0
    Heterogen Atoms 192
    Solvent Atoms 84
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution Phaser
    Structure Refinement PHENIX (phenix.refine: 1.6.1_357)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.1_357)
    model building Phaser
    data collection HKL-2000