POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4H4M
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 277.0
    Details 20% (w/v) PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5 mM spermine-HCl, 50 mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 225.13 α = 90
    b = 69.21 β = 106.43
    c = 104.14 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 77
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Details Monochromator
    Collection Date 2012-08-03
     
    Diffraction Radiation
    Monochromator Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror.
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.075
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.5
    Observed Criterion Sigma(I) 1.5
    Resolution(High) 2.85
    Resolution(Low) 36.64
    Number Reflections(All) 35694
    Number Reflections(Observed) 35694
    Percent Possible(Observed) 98.43
    R Merge I(Observed) 0.099
    B(Isotropic) From Wilson Plot 83.42
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 2.85
    Resolution(Low) 2.9
    Percent Possible(All) 98.6
    R Merge I(Observed) 0.411
    Mean I Over Sigma(Observed) 2.7
    R-Sym I(Observed) 0.546
    Redundancy 3.7
    Number Unique Reflections(All) 1780
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.85
    Resolution(Low) 36.639
    Cut-off Sigma(I) 1.35
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 35785
    Number of Reflections(Observed) 35694
    Number of Reflections(R-Free) 1999
    Percent Reflections(Observed) 98.43
    R-Factor(All) 0.2357
    R-Factor(Observed) 0.2334
    R-Work 0.2334
    R-Free 0.2733
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 60.2555
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.85
    Shell Resolution(Low) 2.9212
    Number of Reflections(Observed) 2369
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2369
    R-Factor(R-Work) 0.3191
    R-Factor(R-Free) 0.3642
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9212
    Shell Resolution(Low) 3.0002
    Number of Reflections(Observed) 2398
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2398
    R-Factor(R-Work) 0.3183
    R-Factor(R-Free) 0.353
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0002
    Shell Resolution(Low) 3.0884
    Number of Reflections(Observed) 2383
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2383
    R-Factor(R-Work) 0.3004
    R-Factor(R-Free) 0.3251
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0884
    Shell Resolution(Low) 3.1881
    Number of Reflections(Observed) 2402
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2402
    R-Factor(R-Work) 0.276
    R-Factor(R-Free) 0.3398
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1881
    Shell Resolution(Low) 3.3019
    Number of Reflections(Observed) 2393
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2393
    R-Factor(R-Work) 0.2772
    R-Factor(R-Free) 0.3335
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3019
    Shell Resolution(Low) 3.434
    Number of Reflections(Observed) 2412
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2412
    R-Factor(R-Work) 0.2673
    R-Factor(R-Free) 0.3298
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.434
    Shell Resolution(Low) 3.5902
    Number of Reflections(Observed) 2408
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2408
    R-Factor(R-Work) 0.2778
    R-Factor(R-Free) 0.3223
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5902
    Shell Resolution(Low) 3.7793
    Number of Reflections(Observed) 2423
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2423
    R-Factor(R-Work) 0.2593
    R-Factor(R-Free) 0.3249
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7793
    Shell Resolution(Low) 4.0158
    Number of Reflections(Observed) 2420
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2420
    R-Factor(R-Work) 0.2422
    R-Factor(R-Free) 0.3094
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0158
    Shell Resolution(Low) 4.3254
    Number of Reflections(Observed) 2444
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2444
    R-Factor(R-Work) 0.2146
    R-Factor(R-Free) 0.2334
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3254
    Shell Resolution(Low) 4.7599
    Number of Reflections(Observed) 2415
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2415
    R-Factor(R-Work) 0.1983
    R-Factor(R-Free) 0.2356
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7599
    Shell Resolution(Low) 5.4467
    Number of Reflections(Observed) 2445
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2445
    R-Factor(R-Work) 0.2014
    R-Factor(R-Free) 0.26
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4467
    Shell Resolution(Low) 6.855
    Number of Reflections(Observed) 2470
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2470
    R-Factor(R-Work) 0.2374
    R-Factor(R-Free) 0.2693
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.855
    Shell Resolution(Low) 36.6419
    Number of Reflections(Observed) 2313
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2313
    R-Factor(R-Work) 0.2064
    R-Factor(R-Free) 0.2227
    Percent Reflections(Observed) 91.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.063
    f_plane_restr 0.004
    f_chiral_restr 0.068
    f_angle_d 0.912
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7996
    Nucleic Acid Atoms 0
    Heterogen Atoms 34
    Solvent Atoms 45
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction HKL