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X-RAY DIFFRACTION
Materials and Methods page
3W3S
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 5.6
    Temperature 293.0
    Details 100mM trisodium citrate-HCl, 1.3M ammonium sulfate, 210mM potassium sodium tartrate, 50mM imidazole, 400mM NaCl, 10mM MgCl2, 0.5mM 5'-O-[N-(L-seryl)sulfamoyl]adenosine, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 272.82 α = 90
    b = 272.82 β = 90
    c = 272.82 γ = 90
     
    Space Group
    Space Group Name:    I 4 3 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 90
    Diffrn ID 2
    Data Collection Temperature 90
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 270
    Details mirrors
    Collection Date 2009-11-04
    Detector CCD
    Type ADSC QUANTUM 315r
    Details mirrors
    Collection Date 2009-11-27
     
    Diffraction Radiation
    Monochromator Si
    Diffraction Protocol MAD
    Monochromator Si
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE AR-NE3A
    Wavelength List 1.07186, 1.07227, 1.05404
    Site PHOTON FACTORY
    Beamline AR-NE3A
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE BL-5A
    Wavelength List 0.97848
    Site PHOTON FACTORY
    Beamline BL-5A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -2.0
    Resolution(High) 3.1
    Resolution(Low) 50
    Number Reflections(All) 31746
    Number Reflections(Observed) 31714
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.094
    B(Isotropic) From Wilson Plot 102.66
    Redundancy 15.0
     
    High Resolution Shell Details
    Resolution(High) 3.1
    Resolution(Low) 3.21
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.847
    Mean I Over Sigma(Observed) 3.49
    R-Sym I(Observed) 0.847
    Redundancy 14.6
    Number Unique Reflections(All) 3126
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 3.095
    Resolution(Low) 35.823
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 31729
    Number of Reflections(Observed) 31040
    Number of Reflections(R-Free) 1556
    Percent Reflections(Observed) 97.83
    R-Factor(Observed) 0.2064
    R-Work 0.2036
    R-Free 0.2603
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 128.428
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0954
    Shell Resolution(Low) 3.1952
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2693
    R-Factor(R-Work) 0.3066
    R-Factor(R-Free) 0.3209
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1952
    Shell Resolution(Low) 3.3094
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2671
    R-Factor(R-Work) 0.2762
    R-Factor(R-Free) 0.3422
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3094
    Shell Resolution(Low) 3.4418
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2596
    R-Factor(R-Work) 0.271
    R-Factor(R-Free) 0.3792
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4418
    Shell Resolution(Low) 3.5983
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2590
    R-Factor(R-Work) 0.2478
    R-Factor(R-Free) 0.3134
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5983
    Shell Resolution(Low) 3.7878
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2617
    R-Factor(R-Work) 0.2158
    R-Factor(R-Free) 0.2572
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7878
    Shell Resolution(Low) 4.0248
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 2568
    R-Factor(R-Work) 0.2009
    R-Factor(R-Free) 0.2467
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0248
    Shell Resolution(Low) 4.3351
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.1735
    R-Factor(R-Free) 0.2337
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3351
    Shell Resolution(Low) 4.7704
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2720
    R-Factor(R-Work) 0.1619
    R-Factor(R-Free) 0.2271
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7704
    Shell Resolution(Low) 5.4586
    Number of Reflections(R-Free) 172
    Number of Reflections(R-Work) 2715
    R-Factor(R-Work) 0.1701
    R-Factor(R-Free) 0.2255
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4586
    Shell Resolution(Low) 6.8694
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2746
    R-Factor(R-Work) 0.1984
    R-Factor(R-Free) 0.2453
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.8694
    Shell Resolution(Low) 35.825
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2933
    R-Factor(R-Work) 0.2108
    R-Factor(R-Free) 0.2722
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 16.634
    f_plane_restr 0.007
    f_chiral_restr 0.082
    f_angle_d 1.253
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4363
    Nucleic Acid Atoms 2090
    Heterogen Atoms 85
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution SHARP
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building SHARP
    data collection ADSC version: Quantum