POP-OUT | CLOSE

An Information Portal to 106858 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4GSJ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.1
    Temperature 277.0
    Details 7.2% isopropanol, 50 mM citrate buffer, pH 4.1, 0.1 M potassium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 56.83 α = 90
    b = 74.63 β = 90
    c = 76.47 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 315
    Collection Date 2012-05-03
     
    Diffraction Radiation
    Monochromator double crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 8.2.2
    Wavelength List 0.979
    Site ALS
    Beamline 8.2.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.7
    Resolution(Low) 50
    Number Reflections(All) 36581
    Number Reflections(Observed) 35213
    Percent Possible(Observed) 96.3
    R Merge I(Observed) 0.06
    Redundancy 6.5
     
    High Resolution Shell Details
    Resolution(High) 1.695
    Resolution(Low) 1.76
    Percent Possible(All) 77.4
    R Merge I(Observed) 0.316
    Redundancy 4.0
    Number Unique Reflections(All) 2760
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.695
    Resolution(Low) 45.612
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 36828
    Number of Reflections(Observed) 35168
    Number of Reflections(R-Free) 1757
    Percent Reflections(Observed) 95.5
    R-Factor(All) 0.1777
    R-Factor(Observed) 0.1777
    R-Work 0.176
    R-Free 0.2068
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 30.5885
    Anisotropic B[1][1] -8.1523
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.041
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 8.1113
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.695
    Shell Resolution(Low) 1.7408
    Number of Reflections(R-Free) 77
    Number of Reflections(R-Work) 1806
    R-Factor(R-Work) 0.2623
    R-Factor(R-Free) 0.3202
    Percent Reflections(Observed) 68.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7408
    Shell Resolution(Low) 1.792
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2213
    R-Factor(R-Work) 0.2155
    R-Factor(R-Free) 0.2654
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.792
    Shell Resolution(Low) 1.8499
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2412
    R-Factor(R-Work) 0.2032
    R-Factor(R-Free) 0.2665
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8499
    Shell Resolution(Low) 1.916
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2626
    R-Factor(R-Work) 0.2027
    R-Factor(R-Free) 0.268
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.916
    Shell Resolution(Low) 1.9927
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.1786
    R-Factor(R-Free) 0.2651
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9927
    Shell Resolution(Low) 2.0834
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2671
    R-Factor(R-Work) 0.1761
    R-Factor(R-Free) 0.2197
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0834
    Shell Resolution(Low) 2.1933
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.1716
    R-Factor(R-Free) 0.2157
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1933
    Shell Resolution(Low) 2.3307
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2682
    R-Factor(R-Work) 0.1723
    R-Factor(R-Free) 0.2139
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3307
    Shell Resolution(Low) 2.5106
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2670
    R-Factor(R-Work) 0.1785
    R-Factor(R-Free) 0.2281
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5106
    Shell Resolution(Low) 2.7632
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2704
    R-Factor(R-Work) 0.1912
    R-Factor(R-Free) 0.2239
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7632
    Shell Resolution(Low) 3.163
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2708
    R-Factor(R-Work) 0.1813
    R-Factor(R-Free) 0.1953
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.163
    Shell Resolution(Low) 3.9847
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2738
    R-Factor(R-Work) 0.1605
    R-Factor(R-Free) 0.2018
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9847
    Shell Resolution(Low) 45.6287
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 2841
    R-Factor(R-Work) 0.1665
    R-Factor(R-Free) 0.1728
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.313
    f_plane_restr 0.004
    f_chiral_restr 0.069
    f_angle_d 1.005
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2297
    Nucleic Acid Atoms 0
    Heterogen Atoms 37
    Solvent Atoms 257
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Phaser
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL