POP-OUT | CLOSE

An Information Portal to 110790 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4I1M
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 293.0
    Details 0.1 M Bicine, pH 7.5, 0.75 M lithium chloride, 6% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 152.7 α = 90
    b = 152.7 β = 90
    c = 129.5 γ = 90
     
    Space Group
    Space Group Name:    P 42 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
    Diffrn ID 2
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2011-08-11
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2011-07-11
     
    Diffraction Radiation
    Monochromator double crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
    Monochromator double crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X10SA
    Wavelength List 0.9793
    Site SLS
    Beamline X10SA
    Source SYNCHROTRON
    Type SLS BEAMLINE X10SA
    Wavelength List 1.000
    Site SLS
    Beamline X10SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.8
    Resolution(Low) 49.83
    Number Reflections(All) 38042
    Number Reflections(Observed) 38042
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.081
    B(Isotropic) From Wilson Plot 66.273
    Redundancy 13.29
     
    High Resolution Shell Details
    Resolution(High) 2.8
    Resolution(Low) 2.87
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.737
    Mean I Over Sigma(Observed) 3.51
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.804
    Resolution(Low) 49.831
    Cut-off Sigma(I) -3.0
    Cut-off Sigma(F) 2.02
    Number of Reflections(Observed) 38034
    Number of Reflections(R-Free) 1902
    Percent Reflections(Observed) 99.83
    R-Factor(Observed) 0.2015
    R-Work 0.1995
    R-Free 0.238
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 76.5663
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.804
    Shell Resolution(Low) 2.8746
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2500
    R-Factor(R-Work) 0.2414
    R-Factor(R-Free) 0.3009
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8746
    Shell Resolution(Low) 2.9523
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2529
    R-Factor(R-Work) 0.2397
    R-Factor(R-Free) 0.2673
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9523
    Shell Resolution(Low) 3.0392
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2550
    R-Factor(R-Work) 0.2391
    R-Factor(R-Free) 0.2832
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0392
    Shell Resolution(Low) 3.1373
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2540
    R-Factor(R-Work) 0.2311
    R-Factor(R-Free) 0.2886
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1373
    Shell Resolution(Low) 3.2494
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2553
    R-Factor(R-Work) 0.2442
    R-Factor(R-Free) 0.2782
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2494
    Shell Resolution(Low) 3.3794
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2545
    R-Factor(R-Work) 0.2249
    R-Factor(R-Free) 0.2839
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3794
    Shell Resolution(Low) 3.5332
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2551
    R-Factor(R-Work) 0.2113
    R-Factor(R-Free) 0.2292
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5332
    Shell Resolution(Low) 3.7194
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2577
    R-Factor(R-Work) 0.2063
    R-Factor(R-Free) 0.257
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7194
    Shell Resolution(Low) 3.9524
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2563
    R-Factor(R-Work) 0.1903
    R-Factor(R-Free) 0.2243
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9524
    Shell Resolution(Low) 4.2574
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2577
    R-Factor(R-Work) 0.182
    R-Factor(R-Free) 0.237
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2574
    Shell Resolution(Low) 4.6855
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2598
    R-Factor(R-Work) 0.1743
    R-Factor(R-Free) 0.2151
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6855
    Shell Resolution(Low) 5.3629
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2613
    R-Factor(R-Work) 0.185
    R-Factor(R-Free) 0.2305
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3629
    Shell Resolution(Low) 6.754
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.2211
    R-Factor(R-Free) 0.2516
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.754
    Shell Resolution(Low) 49.8386
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2788
    R-Factor(R-Work) 0.1794
    R-Factor(R-Free) 0.205
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.172
    f_plane_restr 0.003
    f_chiral_restr 0.051
    f_angle_d 0.676
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6483
    Nucleic Acid Atoms 0
    Heterogen Atoms 7
    Solvent Atoms 28
     
     
  •   Software and Computing Hide
    Computing
    Data Collection XDS
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution SOLVE
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    phasing SOLVE version: 2.13
    data reduction Xscale