POP-OUT | CLOSE

An Information Portal to 110071 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3NKY
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.6
    Temperature 293.0
    Details 35% PEG 4000, 0.2M sodium acetate, 0.1M sodium citrate, 4% butyrolactone, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 93.53 α = 90
    b = 93.53 β = 90
    c = 121.01 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210
    Collection Date 2008-07-04
     
    Diffraction Radiation
    Monochromator diamond monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-1
    Wavelength List 0.933
    Site ESRF
    Beamline ID14-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.28
    Resolution(Low) 46.76
    Number Reflections(Observed) 24188
    Percent Possible(Observed) 96.6
    R Merge I(Observed) 0.076
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.28
    Resolution(Low) 46.76
    Number of Reflections(Observed) 22889
    Number of Reflections(R-Free) 1237
    Percent Reflections(Observed) 96.05
    R-Factor(Observed) 0.24082
    R-Work 0.23957
    R-Free 0.26472
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 52.332
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.28
    Shell Resolution(Low) 2.339
    Number of Reflections(R-Free) 99
    Number of Reflections(R-Work) 1433
    R-Factor(R-Work) 0.332
    R-Factor(R-Free) 0.381
    Percent Reflections(Observed) 85.78
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 0.752
    r_scbond_it 0.435
    r_mcangle_it 0.418
    r_mcbond_it 0.223
    r_gen_planes_refined 0.003
    r_chiral_restr 0.058
    r_dihedral_angle_4_deg 12.174
    r_dihedral_angle_3_deg 14.837
    r_dihedral_angle_2_deg 34.146
    r_dihedral_angle_1_deg 4.476
    r_angle_refined_deg 0.856
    r_bond_refined_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3731
    Nucleic Acid Atoms 0
    Heterogen Atoms 2
    Solvent Atoms 49
     
     
  •   Software and Computing Hide
    Computing
    Data Collection mxCUBE
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution Refmac (rigid body refinement)
    Structure Refinement REFMAC 5.5.0102
     
    Software
    refinement REFMAC version: 5.5.0102
    model building Refmac version: (rigid body refinement)
    data collection mxCUBE