POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4M3X
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    pH 6.5
    Temperature 298.0
    Details 150 mM CaCl2, 12% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate (pH 6.5) , VAPOR DIFFUSION, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 75.12 α = 90
    b = 119.82 β = 90
    c = 130.27 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 110
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-10-12
     
    Diffraction Radiation
    Monochromator graphite
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-E
    Wavelength List 0.97
    Site APS
    Beamline 24-ID-E
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.2
    Observed Criterion Sigma(I) 1.1
    Resolution(High) 2.2
    Resolution(Low) 50
    Number Reflections(All) 56211
    Number Reflections(Observed) 53321
    Percent Possible(Observed) 94.9
     
    High Resolution Shell Details
    Resolution(High) 2.2
    Resolution(Low) 2.3
    Percent Possible(All) 92.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.2
    Resolution(Low) 49.26
    Number of Reflections(Observed) 53321
    Number of Reflections(R-Free) 2857
    Percent Reflections(Observed) 92.44
    R-Factor(Observed) 0.19348
    R-Work 0.19086
    R-Free 0.24148
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 36.033
    Anisotropic B[1][1] -4.08
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 3.38
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.7
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.196
    Shell Resolution(Low) 2.253
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 3740
    R-Factor(R-Work) 0.258
    R-Factor(R-Free) 0.341
    Percent Reflections(Observed) 88.63
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.005
    r_chiral_restr 0.075
    r_dihedral_angle_4_deg 13.692
    r_dihedral_angle_3_deg 14.846
    r_dihedral_angle_2_deg 34.652
    r_dihedral_angle_1_deg 5.599
    r_angle_other_deg 0.867
    r_angle_refined_deg 1.172
    r_bond_other_d 0.001
    r_bond_refined_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7340
    Nucleic Acid Atoms 630
    Heterogen Atoms 35
    Solvent Atoms 293
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution AMoRE
    Structure Refinement REFMAC 5.7.0029
     
    Software
    refinement REFMAC version: 5.7.0029
    model building AMoRE
    data collection HKL-2000