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X-RAY DIFFRACTION
Materials and Methods page
3VAY
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 277.0
    Details 20~26% PEG4K, 0.2M MgCl2.6H2O, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 44.33 α = 90
    b = 92.27 β = 108.13
    c = 70.19 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 ADSC QUANTUM 315r
    Collection Date 2011-06-08
     
    Diffraction Radiation
    Monochromator Double Crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 1.7
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 1.98
    Resolution(Low) 50
    Number Reflections(All) 37428
    Number Reflections(Observed) 35295
    Percent Possible(Observed) 94.3
    R Merge I(Observed) 0.09
    B(Isotropic) From Wilson Plot 25.3
    Redundancy 14.6
     
    High Resolution Shell Details
    Resolution(High) 1.98
    Resolution(Low) 2.05
    Percent Possible(All) 90.6
    R Merge I(Observed) 0.454
    Mean I Over Sigma(Observed) 6.6
    Redundancy 14.7
    Number Unique Reflections(All) 3770
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 1.979
    Resolution(Low) 25.912
    Cut-off Sigma(F) 1.36
    Number of Reflections(all) 37458
    Number of Reflections(Observed) 35241
    Number of Reflections(R-Free) 1755
    Percent Reflections(Observed) 94.08
    R-Factor(All) 0.2067
    R-Factor(Observed) 0.1945
    R-Work 0.193
    R-Free 0.224
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 29.7
    Anisotropic B[1][1] 0.694
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.5125
    Anisotropic B[2][2] 0.7704
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.4644
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9793
    Shell Resolution(Low) 2.05
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 3198
    R-Factor(R-Work) 0.236
    R-Factor(R-Free) 0.264
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.05
    Shell Resolution(Low) 2.132
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 3241
    R-Factor(R-Work) 0.2141
    R-Factor(R-Free) 0.2643
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.132
    Shell Resolution(Low) 2.229
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 3264
    R-Factor(R-Work) 0.2076
    R-Factor(R-Free) 0.2722
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.229
    Shell Resolution(Low) 2.3464
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 3302
    R-Factor(R-Work) 0.1979
    R-Factor(R-Free) 0.2273
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3464
    Shell Resolution(Low) 2.4933
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3311
    R-Factor(R-Work) 0.203
    R-Factor(R-Free) 0.2636
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4933
    Shell Resolution(Low) 2.6857
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 3368
    R-Factor(R-Work) 0.2094
    R-Factor(R-Free) 0.2401
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6857
    Shell Resolution(Low) 2.9556
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 3392
    R-Factor(R-Work) 0.2172
    R-Factor(R-Free) 0.25
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9556
    Shell Resolution(Low) 3.3825
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 3415
    R-Factor(R-Work) 0.2049
    R-Factor(R-Free) 0.2463
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3825
    Shell Resolution(Low) 4.2585
    Number of Reflections(R-Free) 199
    Number of Reflections(R-Work) 3433
    R-Factor(R-Work) 0.168
    R-Factor(R-Free) 0.1826
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2585
    Shell Resolution(Low) 25.9142
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 3562
    R-Factor(R-Work) 0.1716
    R-Factor(R-Free) 0.1879
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.748
    f_plane_restr 0.005
    f_chiral_restr 0.087
    f_angle_d 1.105
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3603
    Nucleic Acid Atoms 0
    Heterogen Atoms 17
    Solvent Atoms 325
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX(phenix.autosol)
    Structure Refinement PHENIX (phenix.refine: 1.6.4_486)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.4_486)
    model building PHENIX(phenix.autosol)
    data collection HKL-2000