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X-RAY DIFFRACTION
Materials and Methods page
4GYS
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 298.0
    Details 1.04M sodium malonate,100mM PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 77.7 α = 90
    b = 77.7 β = 90
    c = 395.47 γ = 120
     
    Space Group
    Space Group Name:    P 61
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2011-01-01
     
    Diffraction Radiation
    Monochromator Si (111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-G
    Wavelength List 1.033
    Site APS
    Beamline 21-ID-G
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.2
    Resolution(Low) 50
    Number Reflections(All) 66210
    Number Reflections(Observed) 66038
    Percent Possible(Observed) 97.1
    R Merge I(Observed) 0.115
    B(Isotropic) From Wilson Plot 31.5
    Redundancy 9.2
     
    High Resolution Shell Details
    Resolution(High) 2.2
    Resolution(Low) 2.24
    Percent Possible(All) 96.2
    R Merge I(Observed) 0.332
    Mean I Over Sigma(Observed) 4.9
    Redundancy 6.6
    Number Unique Reflections(All) 3285
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.201
    Resolution(Low) 38.85
    Cut-off Sigma(F) 1.36
    Number of Reflections(Observed) 66038
    Number of Reflections(R-Free) 2005
    Percent Reflections(Observed) 97.11
    R-Factor(Observed) 0.1784
    R-Work 0.1776
    R-Free 0.2027
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 7.7477
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 7.7477
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -12.7296
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2009
    Shell Resolution(Low) 2.2559
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 4547
    R-Factor(R-Work) 0.2178
    R-Factor(R-Free) 0.2745
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2559
    Shell Resolution(Low) 2.3169
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 4713
    R-Factor(R-Work) 0.2007
    R-Factor(R-Free) 0.2602
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3169
    Shell Resolution(Low) 2.385
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 4671
    R-Factor(R-Work) 0.1873
    R-Factor(R-Free) 0.2281
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.385
    Shell Resolution(Low) 2.462
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 4697
    R-Factor(R-Work) 0.187
    R-Factor(R-Free) 0.2526
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.462
    Shell Resolution(Low) 2.55
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 4724
    R-Factor(R-Work) 0.1907
    R-Factor(R-Free) 0.2354
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.55
    Shell Resolution(Low) 2.6521
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 4693
    R-Factor(R-Work) 0.1909
    R-Factor(R-Free) 0.2011
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6521
    Shell Resolution(Low) 2.7727
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 4739
    R-Factor(R-Work) 0.1989
    R-Factor(R-Free) 0.262
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7727
    Shell Resolution(Low) 2.9189
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 4667
    R-Factor(R-Work) 0.2022
    R-Factor(R-Free) 0.2704
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9189
    Shell Resolution(Low) 3.1017
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 4725
    R-Factor(R-Work) 0.1879
    R-Factor(R-Free) 0.2259
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1017
    Shell Resolution(Low) 3.341
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 4615
    R-Factor(R-Work) 0.1726
    R-Factor(R-Free) 0.1924
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.341
    Shell Resolution(Low) 3.677
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 4421
    R-Factor(R-Work) 0.1591
    R-Factor(R-Free) 0.1685
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.677
    Shell Resolution(Low) 4.2086
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 4109
    R-Factor(R-Work) 0.1503
    R-Factor(R-Free) 0.1696
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2086
    Shell Resolution(Low) 5.3002
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 4160
    R-Factor(R-Work) 0.1555
    R-Factor(R-Free) 0.1674
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3002
    Shell Resolution(Low) 38.8565
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 4554
    R-Factor(R-Work) 0.1863
    R-Factor(R-Free) 0.1784
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.08
    f_dihedral_angle_d 13.59
    f_angle_d 1.277
    f_bond_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6819
    Nucleic Acid Atoms 0
    Heterogen Atoms 28
    Solvent Atoms 426
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MC-2 diffractometer software from EMBL
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Phnix.autoMR
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building Phnix.autoMR
    data collection MC-2 version: diffractometer software from EMBL