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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3EXX
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 6.4
    Temperature 291.0
    Details 1 mM sodium citrate, 10% acetone, 15 mM nickel(II) acetate tetrahydrate, pH 6.4, vapor diffusion, hanging drop, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 81.41 α = 90
    b = 81.41 β = 90
    c = 33.75 γ = 120
     
    Space Group
    Space Group Name:    H 3
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Collection Date 2002-10-28
     
    Diffraction Radiation
    Monochromator The optics consist in a vertical collimating mirror, a double-crystal Si(111) monochromator followed by a toroidal bendable focussing mirror.
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ELETTRA BEAMLINE 5.2R
    Wavelength List 1.00
    Site ELETTRA
    Beamline 5.2R
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.35
    Resolution(Low) 16.41
    Number Reflections(All) 29352
    Number Reflections(Observed) 18240
    Percent Possible(Observed) 99.7
     
    High Resolution Shell Details
    Resolution(High) 1.35
    Resolution(Low) 1.385
    Percent Possible(All) 100.0
     
     
  •   Refinement Hide
    Refinement Statistics
    reflnsShellList 1.35
    Resolution(Low) 16.41
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 18240
    Number of Reflections(Observed) 18240
    Number of Reflections(R-Free) 935
    Percent Reflections(Observed) 99.7
    R-Factor(All) 0.126
    R-Factor(Observed) 0.126
    R-Work 0.124
    R-Free 0.171
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 15.198
    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] -0.01
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.35
    Shell Resolution(Low) 1.385
    Number of Reflections(R-Free) 63
    Number of Reflections(R-Work) 1277
    R-Factor(R-Work) 0.13
    R-Factor(R-Free) 0.227
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 7.482
    r_sphericity_free 10.719
    r_rigid_bond_restr 2.93
    r_bond_refined_d 0.028
    r_angle_refined_deg 2.15
    r_dihedral_angle_1_deg 21.571
    r_dihedral_angle_2_deg 34.246
    r_dihedral_angle_3_deg 13.042
    r_dihedral_angle_4_deg 9.224
    r_chiral_restr 0.17
    r_gen_planes_refined 0.013
    r_mcbond_it 2.778
    r_mcangle_it 3.891
    r_scbond_it 5.041
    r_scangle_it 6.722
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 810
    Nucleic Acid Atoms 0
    Heterogen Atoms 4
    Solvent Atoms 151
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Refinement REFMAC 5.4.0067
     
    Software
    data extraction pdb_extract version: 3.006
    refinement REFMAC5 version: 5.4.0067
    data processing SCALA
    collection/data indexing Mosflm