POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
3VB7
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.5
    Temperature 289.0
    Details 8.5% PEG 6000, 0.1M MES, 1mM DTT, 1mM EDTA, 3% DMSO, 10% Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 52.32 α = 90
    b = 96.49 β = 103.3
    c = 67.64 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 IMAGE PLATE
    Type RIGAKU RAXIS IV
    Collection Date 2009-10-17
     
    Diffraction Radiation
    Monochromator YALE MIRRORS
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU FR-E+ SUPERBRIGHT
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.95
    Resolution(Low) 24.61
    Number Reflections(Observed) 46922
    Percent Possible(Observed) 98.6
    B(Isotropic) From Wilson Plot 25.71
     
    High Resolution Shell Details
    Resolution(High) 1.95
    Resolution(Low) 2.06
    Percent Possible(All) 98.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.95
    Resolution(Low) 24.614
    Cut-off Sigma(F) 1.42
    Number of Reflections(Observed) 46888
    Number of Reflections(R-Free) 1999
    Percent Reflections(Observed) 98.45
    R-Factor(All) 0.206
    R-Factor(Observed) 0.1893
    R-Work 0.1875
    R-Free 0.2304
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 29.7245
    Anisotropic B[1][1] 1.4721
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 4.9941
    Anisotropic B[2][2] 1.304
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -2.7761
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.95
    Shell Resolution(Low) 1.9988
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 3131
    R-Factor(R-Work) 0.2429
    R-Factor(R-Free) 0.3061
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9988
    Shell Resolution(Low) 2.0528
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 3119
    R-Factor(R-Work) 0.2076
    R-Factor(R-Free) 0.251
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0528
    Shell Resolution(Low) 2.1131
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3164
    R-Factor(R-Work) 0.1812
    R-Factor(R-Free) 0.2537
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1131
    Shell Resolution(Low) 2.1813
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 3169
    R-Factor(R-Work) 0.1813
    R-Factor(R-Free) 0.2199
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1813
    Shell Resolution(Low) 2.2592
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 3166
    R-Factor(R-Work) 0.1882
    R-Factor(R-Free) 0.2639
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2592
    Shell Resolution(Low) 2.3496
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3174
    R-Factor(R-Work) 0.1948
    R-Factor(R-Free) 0.2502
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3496
    Shell Resolution(Low) 2.4564
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3204
    R-Factor(R-Work) 0.1914
    R-Factor(R-Free) 0.2474
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4564
    Shell Resolution(Low) 2.5858
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 3215
    R-Factor(R-Work) 0.1951
    R-Factor(R-Free) 0.267
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5858
    Shell Resolution(Low) 2.7476
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3228
    R-Factor(R-Work) 0.1946
    R-Factor(R-Free) 0.2471
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7476
    Shell Resolution(Low) 2.9595
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 3222
    R-Factor(R-Work) 0.1898
    R-Factor(R-Free) 0.2436
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9595
    Shell Resolution(Low) 3.2567
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3257
    R-Factor(R-Work) 0.1867
    R-Factor(R-Free) 0.2327
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2567
    Shell Resolution(Low) 3.7265
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3256
    R-Factor(R-Work) 0.1811
    R-Factor(R-Free) 0.23
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7265
    Shell Resolution(Low) 4.6897
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3270
    R-Factor(R-Work) 0.1647
    R-Factor(R-Free) 0.195
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6897
    Shell Resolution(Low) 24.6163
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 3314
    R-Factor(R-Work) 0.1985
    R-Factor(R-Free) 0.2059
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.079
    f_dihedral_angle_d 13.942
    f_angle_d 1.113
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4761
    Nucleic Acid Atoms 0
    Heterogen Atoms 18
    Solvent Atoms 282
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CrystalClear
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASES
    Structure Refinement PHENIX (phenix.refine: 1.6.4_486)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.4_486)
    model building PHASES
    data collection CrystalClear