POP-OUT | CLOSE

An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4II5
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 293.15
    Details 22% W/V POLYACRYLIC ACID SODIUM SALT 5100, 20MM MGCL2, 100MM HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 71.14 α = 90
    b = 164.14 β = 107.04
    c = 73.45 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2010-03-22
     
    Diffraction Radiation
    Monochromator DIAMOND LAUE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-G
    Wavelength List 0.97872
    Site APS
    Beamline 21-ID-G
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 1.5
    Resolution(High) 2.15
    Resolution(Low) 29.56
    Number Reflections(Observed) 83087
    Percent Possible(Observed) 95.3
    B(Isotropic) From Wilson Plot 32.8
    Redundancy 3.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.15
    Resolution(Low) 29.56
    Cut-off Sigma(I) 1.5
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 83087
    Number of Reflections(R-Free) 2007
    Percent Reflections(Observed) 95.3
    R-Factor(All) 0.2004
    R-Factor(Observed) 0.2004
    R-Work 0.1997
    R-Free 0.2262
    R-Free Selection Details PHENIX selected about 2000 reflections distributed roughly equally among the shells
     
    Temperature Factor Modeling
    Isotropic Thermal Model isotropic plus TLS
    Mean Isotropic B Value 45.2
    Anisotropic B[1][1] 9.618
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 5.181
    Anisotropic B[2][2] -7.6602
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.9577
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.15
    Shell Resolution(Low) 2.2038
    Number of Reflections(Observed) 5219
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 5219
    R-Factor(R-Work) 0.3383
    R-Factor(R-Free) 0.3501
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2038
    Shell Resolution(Low) 2.2633
    Number of Reflections(Observed) 5281
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 5281
    R-Factor(R-Work) 0.3168
    R-Factor(R-Free) 0.3139
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2633
    Shell Resolution(Low) 2.3299
    Number of Reflections(Observed) 5433
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 5433
    R-Factor(R-Work) 0.2879
    R-Factor(R-Free) 0.3302
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3299
    Shell Resolution(Low) 2.4051
    Number of Reflections(Observed) 5544
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 5544
    R-Factor(R-Work) 0.2576
    R-Factor(R-Free) 0.254
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4051
    Shell Resolution(Low) 2.491
    Number of Reflections(Observed) 5663
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 5663
    R-Factor(R-Work) 0.255
    R-Factor(R-Free) 0.3038
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.491
    Shell Resolution(Low) 2.5907
    Number of Reflections(Observed) 5860
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 5860
    R-Factor(R-Work) 0.2333
    R-Factor(R-Free) 0.2928
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5907
    Shell Resolution(Low) 2.7085
    Number of Reflections(Observed) 5902
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 5902
    R-Factor(R-Work) 0.2245
    R-Factor(R-Free) 0.2491
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7085
    Shell Resolution(Low) 2.8512
    Number of Reflections(Observed) 5994
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 5994
    R-Factor(R-Work) 0.1965
    R-Factor(R-Free) 0.2339
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8512
    Shell Resolution(Low) 3.0296
    Number of Reflections(Observed) 5991
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 5991
    R-Factor(R-Work) 0.1913
    R-Factor(R-Free) 0.2437
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0296
    Shell Resolution(Low) 3.2633
    Number of Reflections(Observed) 5995
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 5995
    R-Factor(R-Work) 0.1822
    R-Factor(R-Free) 0.2277
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2633
    Shell Resolution(Low) 3.5912
    Number of Reflections(Observed) 6036
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 6036
    R-Factor(R-Work) 0.1809
    R-Factor(R-Free) 0.2258
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5912
    Shell Resolution(Low) 4.1096
    Number of Reflections(Observed) 6048
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 6048
    R-Factor(R-Work) 0.1708
    R-Factor(R-Free) 0.211
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1096
    Shell Resolution(Low) 5.1732
    Number of Reflections(Observed) 6045
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 6045
    R-Factor(R-Work) 0.155
    R-Factor(R-Free) 0.1557
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1732
    Shell Resolution(Low) 29.56
    Number of Reflections(Observed) 6069
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 6069
    R-Factor(R-Work) 0.1929
    R-Factor(R-Free) 0.1933
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.086
    f_dihedral_angle_d 16.036
    f_angle_d 1.168
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 8896
    Nucleic Acid Atoms 0
    Heterogen Atoms 104
    Solvent Atoms 517
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7_650)
    model building PHASER
    data collection MAR345dtb