POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4F5F
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5
    Temperature 277.0
    Details 8% PEG 4000, 0.1 M Sodium Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 60.19 α = 90
    b = 103.68 β = 90
    c = 138.9 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 85
     
    Diffraction Detector
    Detector CCD
    Type BRUKER SMART 6000
    Details mirrors
    Collection Date 2010-08-18
     
    Diffraction Radiation
    Monochromator Osmic Mirrors
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RU300
    Wavelength List 1.54
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.25
    Resolution(Low) 57.7
    Number Reflections(All) 42133
    Number Reflections(Observed) 41556
    Percent Possible(Observed) 98.6
    R Merge I(Observed) 0.0869
    B(Isotropic) From Wilson Plot 25.2
    Redundancy 4.91
     
    High Resolution Shell Details
    Resolution(High) 2.25
    Resolution(Low) 2.34
    Percent Possible(All) 87.5
    R Merge I(Observed) 0.3248
    Mean I Over Sigma(Observed) 2.53
    R-Sym I(Observed) 0.3248
    Redundancy 2.35
    Number Unique Reflections(All) 4018
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.25
    Resolution(Low) 57.703
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 41479
    Number of Reflections(R-Free) 2013
    Percent Reflections(Observed) 98.61
    R-Factor(Observed) 0.1761
    R-Work 0.1743
    R-Free 0.2133
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 5.5539
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.5501
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -5.0037
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.25
    Shell Resolution(Low) 2.3063
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2325
    R-Factor(R-Work) 0.2012
    R-Factor(R-Free) 0.2358
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3063
    Shell Resolution(Low) 2.3686
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2736
    R-Factor(R-Work) 0.2067
    R-Factor(R-Free) 0.2649
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3686
    Shell Resolution(Low) 2.4384
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2805
    R-Factor(R-Work) 0.1968
    R-Factor(R-Free) 0.2655
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4384
    Shell Resolution(Low) 2.5171
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2839
    R-Factor(R-Work) 0.1946
    R-Factor(R-Free) 0.2393
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5171
    Shell Resolution(Low) 2.607
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2817
    R-Factor(R-Work) 0.192
    R-Factor(R-Free) 0.2485
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.607
    Shell Resolution(Low) 2.7114
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2811
    R-Factor(R-Work) 0.1789
    R-Factor(R-Free) 0.1965
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7114
    Shell Resolution(Low) 2.8348
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2822
    R-Factor(R-Work) 0.1688
    R-Factor(R-Free) 0.2422
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8348
    Shell Resolution(Low) 2.9842
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2860
    R-Factor(R-Work) 0.1784
    R-Factor(R-Free) 0.1887
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9842
    Shell Resolution(Low) 3.1712
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 2838
    R-Factor(R-Work) 0.1745
    R-Factor(R-Free) 0.2214
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1712
    Shell Resolution(Low) 3.416
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2841
    R-Factor(R-Work) 0.1702
    R-Factor(R-Free) 0.2002
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.416
    Shell Resolution(Low) 3.7597
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2899
    R-Factor(R-Work) 0.1672
    R-Factor(R-Free) 0.233
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7597
    Shell Resolution(Low) 4.3036
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2889
    R-Factor(R-Work) 0.1479
    R-Factor(R-Free) 0.1646
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3036
    Shell Resolution(Low) 5.4215
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2925
    R-Factor(R-Work) 0.1464
    R-Factor(R-Free) 0.1798
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4215
    Shell Resolution(Low) 57.722
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 3059
    R-Factor(R-Work) 0.1968
    R-Factor(R-Free) 0.218
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.07
    f_dihedral_angle_d 13.769
    f_angle_d 1.045
    f_bond_d 0.007
     
    Coordinate Error
    Luzzati Sigma A(Observed) 0.59
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6202
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 697
     
     
  •   Software and Computing Hide
    Computing
    Data Collection PROTEUM PLUS
    Data Reduction (intensity integration) PROTEUM PLUS
    Data Reduction (data scaling) PROTEUM PLUS
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building PHASER
    data collection PROTEUM version: PLUS