POP-OUT | CLOSE

An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2AKR
  •   Crystallization Hide
    Crystallization Experiments
    pH 6.5
    Temperature 277.0
    Details ammonium sulfate, NaCl, sodium cacodylate, manganese chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K, pH 6.50
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 58.86 α = 90
    b = 74.84 β = 102.1
    c = 101.56 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 120
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2005-04-15
     
    Diffraction Radiation
    Monochromator CURVED CRYSTAL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL11-1
    Wavelength 0.97976
    Site SSRL
    Beamline BL11-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.9
    Resolution(Low) 50
    Number Reflections(Observed) 67171
    Percent Possible(Observed) 98.7
    B(Isotropic) From Wilson Plot 19.8
    Redundancy 2.4
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 1.97
    Percent Possible(All) 99.7
    Mean I Over Sigma(Observed) 2.4
    R-Sym I(Observed) 0.58
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.9
    Resolution(Low) 41.38
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 67104
    Number of Reflections(Observed) 65745
    Number of Reflections(R-Free) 1359
    Percent Reflections(Observed) 98.6
    R-Factor(Observed) 0.187
    R-Work 0.186
    R-Free 0.249
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 27.481
    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] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9
    Shell Resolution(Low) 1.95
    Number of Reflections(R-Free) 99
    Number of Reflections(R-Work) 4796
    R-Factor(R-Work) 0.262
    R-Factor(R-Free) 0.336
    Percent Reflections(Observed) 98.37
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.771
    r_scbond_it 2.524
    r_mcangle_it 1.517
    r_mcbond_it 1.012
    r_nbd_refined 0.215
    r_gen_planes_refined 0.007
    r_chiral_restr 0.141
    r_dihedral_angle_4_deg 22.316
    r_dihedral_angle_3_deg 16.911
    r_dihedral_angle_2_deg 34.604
    r_dihedral_angle_1_deg 6.409
    r_angle_refined_deg 1.749
    r_bond_refined_d 0.016
    r_nbtor_refined 0.311
    r_xyhbond_nbd_refined 0.2
    r_symmetry_vdw_refined 0.213
    r_symmetry_hbond_refined 0.283
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5950
    Nucleic Acid Atoms 0
    Heterogen Atoms 220
    Solvent Atoms 748
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) CCP4 (TRUNCATE)
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.2.0003
     
    Software
    refinement REFMAC version: 5.2.0003