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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4EB0
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7
    Temperature 293.0
    Details 20% (w/v) polyethylene glycol (PEG) 3350, 200mM sodium thiocyanate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 40.91 α = 90
    b = 71.08 β = 90
    c = 72.73 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 BRUKER SMART 6500
    Collection Date 2011-10-10
     
    Diffraction Radiation
    Monochromator horizontal focusing mirror
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL44XU
    Wavelength List 0.9
    Site SPRING-8
    Beamline BL44XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.5
    Resolution(Low) 50
    Number Reflections(Observed) 35110
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.106
    Redundancy 13.7
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.53
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.419
    Mean I Over Sigma(Observed) 0.419
    R-Sym I(Observed) 0.419
    Redundancy 12.7
    Number Unique Reflections(All) 1742
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.5
    Resolution(Low) 50.0
    Number of Reflections(Observed) 32818
    Number of Reflections(R-Free) 1741
    Percent Reflections(Observed) 99.56
    R-Factor(Observed) 0.15801
    R-Work 0.15654
    R-Free 0.1863
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 17.172
    Anisotropic B[1][1] -0.67
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.04
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.7
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5
    Shell Resolution(Low) 1.539
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2374
    R-Factor(R-Work) 0.188
    R-Factor(R-Free) 0.25
    Percent Reflections(Observed) 99.64
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.458
    r_scbond_it 3.398
    r_mcangle_it 2.175
    r_mcbond_it 1.466
    r_gen_planes_refined 0.02
    r_chiral_restr 0.084
    r_dihedral_angle_4_deg 12.062
    r_dihedral_angle_3_deg 10.84
    r_dihedral_angle_2_deg 32.304
    r_dihedral_angle_1_deg 7.429
    r_angle_refined_deg 1.0
    r_bond_refined_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1962
    Nucleic Acid Atoms 0
    Heterogen Atoms 12
    Solvent Atoms 315
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL
    Data Reduction (data scaling) HKL
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.5.0109
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5 version: refmac_5.5.0109
    density modification DM version: 6.1
    molecular replacement MOLREP
    data reduction HKL