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X-RAY DIFFRACTION
Materials and Methods page
3VAQ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    Temperature 293.0
    Details 100mM Bis-tris pH 6.1-6.7, 200mM LiSO4, 16-20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 59.1 α = 90
    b = 180.31 β = 90
    c = 79.43 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Details Compound Refractive Lenses
    Collection Date 2011-09-25
     
    Diffraction Radiation
    Monochromator DCM
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I04
    Wavelength List 0.96110
    Site DIAMOND
    Beamline I04
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.7
    Observed Criterion Sigma(I) 1.7
    Resolution(High) 2.44
    Resolution(Low) 79.43
    Number Reflections(All) 32370
    Number Reflections(Observed) 32370
    Percent Possible(Observed) 99.6
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 2.44
    Resolution(Low) 2.5
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.674
    Mean I Over Sigma(Observed) 1.1
    R-Sym I(Observed) 0.674
    Redundancy 3.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.44
    Resolution(Low) 59.598
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 32370
    Number of Reflections(Observed) 32318
    Number of Reflections(R-Free) 1639
    Percent Reflections(Observed) 99.53
    R-Factor(Observed) 0.1895
    R-Work 0.1873
    R-Free 0.2301
     
    Temperature Factor Modeling
    Mean Isotropic B Value 46.3534
    Anisotropic B[1][1] -8.2041
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 9.9362
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.7256
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.44
    Shell Resolution(Low) 2.5118
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2504
    R-Factor(R-Work) 0.2823
    R-Factor(R-Free) 0.3126
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5118
    Shell Resolution(Low) 2.5929
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2525
    R-Factor(R-Work) 0.2542
    R-Factor(R-Free) 0.3345
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5929
    Shell Resolution(Low) 2.6856
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2530
    R-Factor(R-Work) 0.2403
    R-Factor(R-Free) 0.2682
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6856
    Shell Resolution(Low) 2.7931
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2523
    R-Factor(R-Work) 0.2291
    R-Factor(R-Free) 0.2845
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7931
    Shell Resolution(Low) 2.9202
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2537
    R-Factor(R-Work) 0.2259
    R-Factor(R-Free) 0.2862
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9202
    Shell Resolution(Low) 3.0742
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 2504
    R-Factor(R-Work) 0.205
    R-Factor(R-Free) 0.2576
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0742
    Shell Resolution(Low) 3.2668
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2533
    R-Factor(R-Work) 0.2098
    R-Factor(R-Free) 0.2358
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2668
    Shell Resolution(Low) 3.519
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2547
    R-Factor(R-Work) 0.1854
    R-Factor(R-Free) 0.2131
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.519
    Shell Resolution(Low) 3.873
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2533
    R-Factor(R-Work) 0.1629
    R-Factor(R-Free) 0.2185
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.873
    Shell Resolution(Low) 4.4333
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2550
    R-Factor(R-Work) 0.1565
    R-Factor(R-Free) 0.2115
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4333
    Shell Resolution(Low) 5.5849
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2614
    R-Factor(R-Work) 0.1522
    R-Factor(R-Free) 0.1867
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5849
    Shell Resolution(Low) 59.6162
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2779
    R-Factor(R-Work) 0.1773
    R-Factor(R-Free) 0.1946
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.002
    f_chiral_restr 0.044
    f_dihedral_angle_d 10.855
    f_angle_d 0.574
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5376
    Nucleic Acid Atoms 0
    Heterogen Atoms 40
    Solvent Atoms 152
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    molecular replacement Phaser
    data reduction SCALA version: 3.3.16