POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
3AFA
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 293.0
    Details potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 105.84 α = 90
    b = 109.51 β = 90
    c = 180.92 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2009-11-23
     
    Diffraction Radiation
    Monochromator Double-crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL41XU
    Wavelength List 1.000
    Site SPRING-8
    Beamline BL41XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.5
    Resolution(Low) 50
    Number Reflections(All) 73682
    Number Reflections(Observed) 73546
    Percent Possible(Observed) 99.8
    B(Isotropic) From Wilson Plot 52.4
    Redundancy 7.1
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.54
    Percent Possible(All) 99.7
    Mean I Over Sigma(Observed) 2.8
    R-Sym I(Observed) 0.918
    Redundancy 6.5
    Number Unique Reflections(All) 3623
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 50.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 73400
    Number of Reflections(Observed) 73269
    Number of Reflections(R-Free) 3693
    R-Factor(All) 0.271
    R-Factor(Observed) 0.241
    R-Work 0.24
    R-Free 0.27
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5
    Shell Resolution(Low) 2.59
    Number of Reflections(Observed) 6852
    Number of Reflections(R-Free) 371
    R-Factor(R-Work) 0.325
    R-Factor(R-Free) 0.39
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.59
    Shell Resolution(Low) 2.69
    Number of Reflections(Observed) 6852
    Number of Reflections(R-Free) 362
    R-Factor(R-Work) 0.295
    R-Factor(R-Free) 0.336
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.69
    Shell Resolution(Low) 2.82
    Number of Reflections(Observed) 6888
    Number of Reflections(R-Free) 382
    R-Factor(R-Work) 0.293
    R-Factor(R-Free) 0.361
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.82
    Shell Resolution(Low) 2.96
    Number of Reflections(Observed) 6905
    Number of Reflections(R-Free) 345
    R-Factor(R-Work) 0.274
    R-Factor(R-Free) 0.324
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.96
    Shell Resolution(Low) 3.15
    Number of Reflections(Observed) 6958
    Number of Reflections(R-Free) 330
    R-Factor(R-Work) 0.265
    R-Factor(R-Free) 0.288
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.15
    Shell Resolution(Low) 3.39
    Number of Reflections(Observed) 6924
    Number of Reflections(R-Free) 361
    R-Factor(R-Work) 0.261
    R-Factor(R-Free) 0.306
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.39
    Shell Resolution(Low) 3.73
    Number of Reflections(Observed) 6973
    Number of Reflections(R-Free) 355
    R-Factor(R-Work) 0.234
    R-Factor(R-Free) 0.26
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.73
    Shell Resolution(Low) 4.27
    Number of Reflections(Observed) 6952
    Number of Reflections(R-Free) 402
    R-Factor(R-Work) 0.219
    R-Factor(R-Free) 0.244
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.27
    Shell Resolution(Low) 5.38
    Number of Reflections(Observed) 7056
    Number of Reflections(R-Free) 374
    R-Factor(R-Work) 0.207
    R-Factor(R-Free) 0.233
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.38
    Shell Resolution(Low) 50.0
    Number of Reflections(Observed) 7216
    Number of Reflections(R-Free) 411
    R-Factor(R-Work) 0.217
    R-Factor(R-Free) 0.237
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_improper_angle_d 1.03
    c_dihedral_angle_d 20.2
    c_bond_d 0.006
    c_angle_deg 1.11
     
    Coordinate Error
    Luzzati ESD(Observed) 0.35
    Luzzati Sigma A(Observed) 0.35
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.42
    Luzzati Sigma A(R-Free Set) 0.47
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6023
    Nucleic Acid Atoms 5980
    Heterogen Atoms 12
    Solvent Atoms 183
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BSS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution Molrep
    Structure Refinement CNS 1.2.1
     
    Software
    refinement CNS version: 1.2.1
    model building Molrep
    data collection BSS