POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DV9
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 293.0
    Details 1.7M Li2SO4, 100mM HEPES, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 105.53 α = 90
    b = 128.85 β = 90
    c = 76.77 γ = 90
     
    Space Group
    Space Group Name:    C 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-02-17
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 0.97907
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.08
    Resolution(Low) 35.32
    Number Reflections(All) 31388
    Number Reflections(Observed) 31388
    Percent Possible(Observed) 98.1
    B(Isotropic) From Wilson Plot 14.77
    Redundancy 6.6
     
    High Resolution Shell Details
    Resolution(High) 2.08
    Resolution(Low) 2.19
    Percent Possible(All) 97.9
    R Merge I(Observed) 0.281
    Mean I Over Sigma(Observed) 2.2
    R-Sym I(Observed) 0.281
    Redundancy 5.0
    Number Unique Reflections(All) 4515
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.076
    Resolution(Low) 35.32
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 31388
    Number of Reflections(Observed) 30975
    Number of Reflections(R-Free) 1562
    Percent Reflections(Observed) 96.85
    R-Factor(Observed) 0.1735
    R-Work 0.1716
    R-Free 0.2085
     
    Temperature Factor Modeling
    Mean Isotropic B Value 20.4473
    Anisotropic B[1][1] -5.7888
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 8.1078
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -2.319
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0757
    Shell Resolution(Low) 2.1427
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2535
    R-Factor(R-Work) 0.1971
    R-Factor(R-Free) 0.2378
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1427
    Shell Resolution(Low) 2.2193
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2640
    R-Factor(R-Work) 0.1666
    R-Factor(R-Free) 0.1825
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2193
    Shell Resolution(Low) 2.3081
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2297
    R-Factor(R-Work) 0.1514
    R-Factor(R-Free) 0.2221
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3081
    Shell Resolution(Low) 2.4132
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2700
    R-Factor(R-Work) 0.1603
    R-Factor(R-Free) 0.2023
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4132
    Shell Resolution(Low) 2.5403
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2685
    R-Factor(R-Work) 0.1711
    R-Factor(R-Free) 0.2164
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5403
    Shell Resolution(Low) 2.6995
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2726
    R-Factor(R-Work) 0.1831
    R-Factor(R-Free) 0.2558
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6995
    Shell Resolution(Low) 2.9078
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2718
    R-Factor(R-Work) 0.2013
    R-Factor(R-Free) 0.2541
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9078
    Shell Resolution(Low) 3.2002
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2777
    R-Factor(R-Work) 0.1883
    R-Factor(R-Free) 0.2349
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2002
    Shell Resolution(Low) 3.6629
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 2745
    R-Factor(R-Work) 0.1657
    R-Factor(R-Free) 0.2056
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6629
    Shell Resolution(Low) 4.6133
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2754
    R-Factor(R-Work) 0.1419
    R-Factor(R-Free) 0.1695
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6133
    Shell Resolution(Low) 35.3248
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 2836
    R-Factor(R-Work) 0.1827
    R-Factor(R-Free) 0.1997
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.667
    f_plane_restr 0.004
    f_chiral_restr 0.077
    f_angle_d 1.076
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3022
    Nucleic Acid Atoms 0
    Heterogen Atoms 20
    Solvent Atoms 243
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    molecular replacement Phaser version: 2.3.0
    data reduction SCALA version: 3.3.20