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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1YIK
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    pH 4.5
    Temperature 277.0
    Details Acetate buffer, NaCl, pH 4.5, VAPOR DIFFUSION, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 77.91 α = 90
    b = 77.91 β = 90
    c = 37.76 γ = 90
     
    Space Group
    Space Group Name:    P 43 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
    Collection Date 2004-02-26
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SRS BEAMLINE PX14.2
    Wavelength List 0.97950
    Site SRS
    Beamline PX14.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.75
    Resolution(Low) 55.05
    Number Reflections(All) 81871
    Number Reflections(Observed) 12234
    Percent Possible(Observed) 99.9
     
    High Resolution Shell Details
    Resolution(High) 1.75
    Resolution(Low) 1.84
    Percent Possible(All) 100.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.75
    Resolution(Low) 55.0
    Cut-off Sigma(F) 2.0
    Number of Reflections(all) 12234
    Number of Reflections(Observed) 11619
    Number of Reflections(R-Free) 584
    Percent Reflections(Observed) 99.8
    R-Factor(All) 0.17839
    R-Factor(Observed) 0.17839
    R-Work 0.17565
    R-Free 0.23314
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 19.552
    Anisotropic B[1][1] 0.2
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.2
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.39
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.75
    Shell Resolution(Low) 1.795
    Number of Reflections(R-Free) 54
    Number of Reflections(R-Work) 842
    R-Factor(R-Work) 0.216
    R-Factor(R-Free) 0.329
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.885
    r_scbond_it 2.531
    r_mcangle_it 1.633
    r_mcbond_it 0.939
    r_symmetry_hbond_refined 0.164
    r_symmetry_vdw_refined 0.217
    r_bond_refined_d 0.015
    r_angle_refined_deg 1.577
    r_dihedral_angle_1_deg 6.055
    r_dihedral_angle_2_deg 37.082
    r_dihedral_angle_3_deg 13.273
    r_dihedral_angle_4_deg 19.248
    r_chiral_restr 0.113
    r_gen_planes_refined 0.007
    r_nbd_refined 0.224
    r_nbtor_refined 0.297
    r_xyhbond_nbd_refined 0.155
    r_metal_ion_refined 0.123
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1001
    Nucleic Acid Atoms 0
    Heterogen Atoms 45
    Solvent Atoms 169
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) CCP4 (SCALA)
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.2.0003
     
    Software
    refinement REFMAC version: 5.2.0003