POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4JVB
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 4.6
    Temperature 293.0
    Details 100mM Sodium Acetate, 2.0M NaCl, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 55.68 α = 90
    b = 55.68 β = 90
    c = 116.55 γ = 120
     
    Space Group
    Space Group Name:    P 32 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2011-08-12
     
    Diffraction Radiation
    Monochromator SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X10SA
    Wavelength List 1
    Site SLS
    Beamline X10SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.75
    Resolution(Low) 27.84
    Number Reflections(All) 21768
    Number Reflections(Observed) 21768
    Percent Possible(Observed) 99.8
     
    High Resolution Shell Details
    Resolution(High) 1.75
    Resolution(Low) 1.8
    Percent Possible(All) 99.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.75
    Resolution(Low) 27.84
    Number of Reflections(all) 20677
    Number of Reflections(Observed) 20677
    Number of Reflections(R-Free) 1089
    Percent Reflections(Observed) 99.75
    R-Factor(Observed) 0.19011
    R-Work 0.18771
    R-Free 0.23588
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 31.822
    Anisotropic B[1][1] 1.11
    Anisotropic B[1][2] 0.55
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.11
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.66
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.75
    Shell Resolution(Low) 1.795
    Number of Reflections(R-Free) 79
    Number of Reflections(R-Work) 1368
    R-Factor(R-Work) 0.293
    R-Factor(R-Free) 0.319
    Percent Reflections(Observed) 99.59
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.012
    r_chiral_restr 0.183
    r_dihedral_angle_4_deg 20.153
    r_dihedral_angle_3_deg 15.982
    r_dihedral_angle_2_deg 39.31
    r_dihedral_angle_1_deg 6.962
    r_angle_refined_deg 2.483
    r_bond_refined_d 0.026
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1189
    Nucleic Acid Atoms 0
    Heterogen Atoms 43
    Solvent Atoms 156
     
     
  •   Software and Computing Hide
    Computing
    Data Collection PRO DC
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.6.0093
     
    Software
    refinement REFMAC version: 5.6.0093
    model building MOLREP
    data collection PRO version: DC