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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3EKB
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6
    Temperature 293.0
    Details PEG and Magnesium sulphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 60.88 α = 90
    b = 118.69 β = 90
    c = 146.63 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 ADSC QUANTUM 210
    Collection Date 2006-08-01
     
    Diffraction Radiation
    Monochromator diamond
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-1
    Wavelength List 1.0
    Site ESRF
    Beamline ID14-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.1
    Resolution(Low) 20
    Number Reflections(All) 51268
    Number Reflections(Observed) 51268
    Percent Possible(Observed) 86.6
    R Merge I(Observed) 0.07
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.3
    Resolution(Low) 19.68
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 38754
    Number of Reflections(Observed) 38754
    Number of Reflections(R-Free) 2077
    Percent Reflections(Observed) 100.0
    R-Factor(All) 0.21972
    R-Factor(Observed) 0.21972
    R-Work 0.2153
    R-Free 0.30189
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 39.897
    Anisotropic B[1][1] 0.04
    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] -0.04
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.359
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2903
    R-Factor(R-Work) 0.23
    R-Factor(R-Free) 0.373
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.107
    r_scbond_it 2.805
    r_mcangle_it 1.826
    r_mcbond_it 1.141
    r_nbd_refined 0.255
    r_gen_planes_refined 0.009
    r_chiral_restr 0.129
    r_dihedral_angle_4_deg 18.575
    r_dihedral_angle_3_deg 18.016
    r_dihedral_angle_2_deg 37.051
    r_dihedral_angle_1_deg 7.508
    r_angle_refined_deg 2.011
    r_bond_refined_d 0.022
    r_nbtor_refined 0.314
    r_xyhbond_nbd_refined 0.233
    r_symmetry_vdw_refined 0.232
    r_symmetry_hbond_refined 0.229
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7042
    Nucleic Acid Atoms 0
    Heterogen Atoms 86
    Solvent Atoms 294
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019
    data collection ADSC version: Quantum