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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3AL4
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 291.0
    Details 10% PEG 6000, 5% MPD, 0.1M MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 66.02 α = 62.31
    b = 115.19 β = 77.94
    c = 114.99 γ = 81.05
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector AREA DETECTOR
    Type MARMOSAIC 225 mm CCD
    Details MIRRORS
    Collection Date 2010-01-23
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 0.9795
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 1.5
    Resolution(High) 2.87
    Resolution(Low) 50
    Number Reflections(Observed) 64796
    Percent Possible(Observed) 98.0
    R Merge I(Observed) 0.105
    B(Isotropic) From Wilson Plot 56.27
    Redundancy 3.7
     
    High Resolution Shell Details
    Resolution(High) 2.87
    Resolution(Low) 3.0
    Percent Possible(All) 90.7
    R Merge I(Observed) 0.501
    Mean I Over Sigma(Observed) 1.9
    R-Sym I(Observed) 0.501
    Redundancy 2.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.872
    Resolution(Low) 24.19
    Cut-off Sigma(F) 0.07
    Number of Reflections(Observed) 61067
    Number of Reflections(R-Free) 3085
    Percent Reflections(Observed) 91.6
    R-Factor(Observed) 0.247
    R-Work 0.246
    R-Free 0.27
     
    Temperature Factor Modeling
    Mean Isotropic B Value 81.17
    Anisotropic B[1][1] -5.51
    Anisotropic B[1][2] 2.924
    Anisotropic B[1][3] -2.521
    Anisotropic B[2][2] 0.618
    Anisotropic B[2][3] 17.083
    Anisotropic B[3][3] 4.893
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8716
    Shell Resolution(Low) 2.9164
    Number of Reflections(R-Free) 85
    Number of Reflections(R-Work) 1567
    R-Factor(R-Work) 0.3254
    R-Factor(R-Free) 0.3783
    Percent Reflections(Observed) 57.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9164
    Shell Resolution(Low) 2.9641
    Number of Reflections(R-Free) 116
    Number of Reflections(R-Work) 2233
    R-Factor(R-Work) 0.3179
    R-Factor(R-Free) 0.3668
    Percent Reflections(Observed) 77.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9641
    Shell Resolution(Low) 3.0151
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2338
    R-Factor(R-Work) 0.3152
    R-Factor(R-Free) 0.3527
    Percent Reflections(Observed) 80.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0151
    Shell Resolution(Low) 3.0699
    Number of Reflections(R-Free) 105
    Number of Reflections(R-Work) 2389
    R-Factor(R-Work) 0.317
    R-Factor(R-Free) 0.3285
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0699
    Shell Resolution(Low) 3.1288
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2541
    R-Factor(R-Work) 0.2933
    R-Factor(R-Free) 0.3302
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1288
    Shell Resolution(Low) 3.1925
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2503
    R-Factor(R-Work) 0.2953
    R-Factor(R-Free) 0.3273
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1925
    Shell Resolution(Low) 3.2618
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2574
    R-Factor(R-Work) 0.2911
    R-Factor(R-Free) 0.3123
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2618
    Shell Resolution(Low) 3.3375
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.284
    R-Factor(R-Free) 0.3183
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3375
    Shell Resolution(Low) 3.4207
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2670
    R-Factor(R-Work) 0.2804
    R-Factor(R-Free) 0.3081
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4207
    Shell Resolution(Low) 3.5129
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2697
    R-Factor(R-Work) 0.2782
    R-Factor(R-Free) 0.3091
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5129
    Shell Resolution(Low) 3.616
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2745
    R-Factor(R-Work) 0.2576
    R-Factor(R-Free) 0.3033
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.616
    Shell Resolution(Low) 3.7323
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 2787
    R-Factor(R-Work) 0.2568
    R-Factor(R-Free) 0.2877
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7323
    Shell Resolution(Low) 3.8652
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2823
    R-Factor(R-Work) 0.2484
    R-Factor(R-Free) 0.2488
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8652
    Shell Resolution(Low) 4.0192
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2787
    R-Factor(R-Work) 0.2452
    R-Factor(R-Free) 0.2772
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0192
    Shell Resolution(Low) 4.2013
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 2737
    R-Factor(R-Work) 0.234
    R-Factor(R-Free) 0.2546
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2013
    Shell Resolution(Low) 4.4215
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2915
    R-Factor(R-Work) 0.2247
    R-Factor(R-Free) 0.2494
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4215
    Shell Resolution(Low) 4.6966
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2788
    R-Factor(R-Work) 0.205
    R-Factor(R-Free) 0.2543
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6966
    Shell Resolution(Low) 5.0562
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2862
    R-Factor(R-Work) 0.2196
    R-Factor(R-Free) 0.2618
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0562
    Shell Resolution(Low) 5.5594
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 2826
    R-Factor(R-Work) 0.2089
    R-Factor(R-Free) 0.2304
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5594
    Shell Resolution(Low) 6.3512
    Number of Reflections(R-Free) 172
    Number of Reflections(R-Work) 2821
    R-Factor(R-Work) 0.239
    R-Factor(R-Free) 0.2647
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.3512
    Shell Resolution(Low) 7.9542
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2883
    R-Factor(R-Work) 0.2298
    R-Factor(R-Free) 0.2602
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.9542
    Shell Resolution(Low) 24.188
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2844
    R-Factor(R-Work) 0.1996
    R-Factor(R-Free) 0.194
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.066
    f_dihedral_angle_d 19.606
    f_angle_d 0.971
    f_bond_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 22867
    Nucleic Acid Atoms 0
    Heterogen Atoms 442
    Solvent Atoms 317
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement PHENIX (PHENIX.REFINE: 1.5_2)
     
    Software
    refinement PHENIX version: (PHENIX.REFINE: 1.5_2)
    model building PHASER
    data collection MAR345dtb