POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
3VFX
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 3.8
    Temperature 318.0
    Details Protein Solution: 40mg/ml lysozyme, 50mM sodium acetate, 150mM NaCl, Reservoir Solution: 50mM sodium acetate, 1-1.5M NaCl, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 318K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 31.62 α = 90
    b = 66.44 β = 90
    c = 104.46 γ = 90
     
    Space Group
    Space Group Name:    P 2 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MAR scanner 345 mm plate
    Details Mirrors
    Collection Date 2011-09-19
     
    Diffraction Radiation
    Monochromator Mirrors
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU MICROMAX-007 HF
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.95
    Resolution(Low) 50
    Number Reflections(All) 16785
    Number Reflections(Observed) 16785
    Percent Possible(Observed) 89.6
    R Merge I(Observed) 0.062
    B(Isotropic) From Wilson Plot 21.52
    Redundancy 3.1
     
    High Resolution Shell Details
    Resolution(High) 1.95
    Resolution(Low) 2.02
    Percent Possible(All) 97.4
    R Merge I(Observed) 0.294
    Mean I Over Sigma(Observed) 3.985
    Redundancy 3.1
    Number Unique Reflections(All) 1581
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.95
    Resolution(Low) 23.408
    Cut-off Sigma(I) 2.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 14991
    Number of Reflections(Observed) 14991
    Number of Reflections(R-Free) 755
    Percent Reflections(Observed) 89.58
    R-Factor(Observed) 0.1826
    R-Work 0.1802
    R-Free 0.2265
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model ISOTROPIC
    Mean Isotropic B Value 21.52
    Anisotropic B[1][1] -2.8053
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 5.7249
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -2.9196
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.95
    Shell Resolution(Low) 2.1004
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 3056
    R-Factor(R-Work) 0.1866
    R-Factor(R-Free) 0.2671
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1004
    Shell Resolution(Low) 2.3117
    Number of Reflections(R-Free) 109
    Number of Reflections(R-Work) 2062
    R-Factor(R-Work) 0.2162
    R-Factor(R-Free) 0.3521
    Percent Reflections(Observed) 67.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3117
    Shell Resolution(Low) 2.6458
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 3171
    R-Factor(R-Work) 0.1895
    R-Factor(R-Free) 0.2298
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6458
    Shell Resolution(Low) 3.3319
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3161
    R-Factor(R-Work) 0.1789
    R-Factor(R-Free) 0.2112
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3319
    Shell Resolution(Low) 23.4096
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2786
    R-Factor(R-Work) 0.1664
    R-Factor(R-Free) 0.2009
    Percent Reflections(Observed) 84.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.081
    f_dihedral_angle_d 12.064
    f_angle_d 1.104
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2002
    Nucleic Acid Atoms 0
    Heterogen Atoms 31
    Solvent Atoms 174
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASES
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.2_869)
    model building PHASES
    data collection HKL-2000