POP-OUT | CLOSE

An Information Portal to 108263 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4ELU
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 291.0
    Details 50 mM Na cacodylate pH=6.5, 0.2 M NH4(OAc), 10 mM Mg(OAc)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 108.21 α = 90
    b = 108.21 β = 90
    c = 90.4 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Details Dynamically bendable mirror, LN2 cooled fixed-exit, Si(111) monochromator
    Collection Date 2010-04-22
     
    Diffraction Radiation
    Monochromator LN2 cooled fixed-exit, Si(111) monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06SA
    Wavelength List 1.00
    Site SLS
    Beamline X06SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.79
    Resolution(Low) 50
    Number Reflections(All) 57268
    Number Reflections(Observed) 57268
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.065
     
    High Resolution Shell Details
    Resolution(High) 1.79
    Resolution(Low) 1.9
    Percent Possible(All) 97.3
    R Merge I(Observed) 0.724
    Mean I Over Sigma(Observed) 2.01
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 46.856
    Cut-off Sigma(F) 2.01
    Number of Reflections(all) 56899
    Number of Reflections(Observed) 56899
    Number of Reflections(R-Free) 2857
    Percent Reflections(Observed) 99.98
    R-Factor(Observed) 0.1567
    R-Work 0.1553
    R-Free 0.1825
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Isotropic Thermal Model isotropic and tls
    Anisotropic B[1][1] 6.8621
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 6.8621
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 3.9249
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.8311
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2696
    R-Factor(R-Work) 0.2325
    R-Factor(R-Free) 0.2887
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8311
    Shell Resolution(Low) 1.8644
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.2136
    R-Factor(R-Free) 0.261
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8644
    Shell Resolution(Low) 1.9002
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2665
    R-Factor(R-Work) 0.205
    R-Factor(R-Free) 0.2611
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9002
    Shell Resolution(Low) 1.939
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2685
    R-Factor(R-Work) 0.1891
    R-Factor(R-Free) 0.2301
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.939
    Shell Resolution(Low) 1.9812
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2668
    R-Factor(R-Work) 0.1732
    R-Factor(R-Free) 0.2316
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9812
    Shell Resolution(Low) 2.0273
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2669
    R-Factor(R-Work) 0.1723
    R-Factor(R-Free) 0.2293
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0273
    Shell Resolution(Low) 2.078
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 2679
    R-Factor(R-Work) 0.1656
    R-Factor(R-Free) 0.2277
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.078
    Shell Resolution(Low) 2.1342
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2700
    R-Factor(R-Work) 0.1604
    R-Factor(R-Free) 0.2084
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1342
    Shell Resolution(Low) 2.197
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2679
    R-Factor(R-Work) 0.1528
    R-Factor(R-Free) 0.201
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.197
    Shell Resolution(Low) 2.2679
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2718
    R-Factor(R-Work) 0.149
    R-Factor(R-Free) 0.1892
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2679
    Shell Resolution(Low) 2.3489
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2686
    R-Factor(R-Work) 0.155
    R-Factor(R-Free) 0.2183
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3489
    Shell Resolution(Low) 2.443
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2706
    R-Factor(R-Work) 0.161
    R-Factor(R-Free) 0.2018
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.443
    Shell Resolution(Low) 2.5541
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2677
    R-Factor(R-Work) 0.162
    R-Factor(R-Free) 0.1994
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5541
    Shell Resolution(Low) 2.6888
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.1606
    R-Factor(R-Free) 0.2014
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6888
    Shell Resolution(Low) 2.8572
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2721
    R-Factor(R-Work) 0.1624
    R-Factor(R-Free) 0.1998
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8572
    Shell Resolution(Low) 3.0778
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2718
    R-Factor(R-Work) 0.1575
    R-Factor(R-Free) 0.1888
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0778
    Shell Resolution(Low) 3.3874
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2714
    R-Factor(R-Work) 0.1504
    R-Factor(R-Free) 0.1625
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3874
    Shell Resolution(Low) 3.8774
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 2711
    R-Factor(R-Work) 0.1367
    R-Factor(R-Free) 0.1599
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8774
    Shell Resolution(Low) 4.8843
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2763
    R-Factor(R-Work) 0.1315
    R-Factor(R-Free) 0.1503
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8843
    Shell Resolution(Low) 46.8717
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2853
    R-Factor(R-Work) 0.1673
    R-Factor(R-Free) 0.1674
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.075
    f_dihedral_angle_d 16.431
    f_angle_d 1.188
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4286
    Nucleic Acid Atoms 570
    Heterogen Atoms 131
    Solvent Atoms 380
     
     
  •   Software and Computing Hide
    Computing
    Data Collection XDS
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution PHENIX (phenix.refine: dev_1009)
    Structure Refinement PHENIX (phenix.refine: dev_1009)
     
    Software
    refinement PHENIX version: (phenix.refine: dev_1009)
    model building PHENIX version: (phenix.refine: dev_1009)
    data collection XDS