POP-OUT | CLOSE

An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3FYA
  •   Crystallization Hide
    Crystallization Experiments
    Method precipitation
    pH 8
    Temperature 277.0
    Details 150 mM NaCl, 40 mM Tris-HCl, 5 % w/v glycerol, 2.5 mM CaCl2, pH 8.0, precipitation, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 48.44 α = 90
    b = 48.44 β = 90
    c = 135.78 γ = 120
     
    Space Group
    Space Group Name:    P 65
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
    Collection Date 2008-11-06
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-2
    Wavelength List 0.9330
    Site ESRF
    Beamline ID14-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.95
    Resolution(Low) 41.96
    Number Reflections(All) 3840
    Number Reflections(Observed) 3839
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.263
    B(Isotropic) From Wilson Plot 86.0
    Redundancy 7.6
     
    High Resolution Shell Details
    Resolution(High) 2.95
    Resolution(Low) 3.11
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.412
    Mean I Over Sigma(Observed) 1.9
    R-Sym I(Observed) 0.412
    Redundancy 5.5
    Number Unique Reflections(All) 553
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.0
    Resolution(Low) 35.69
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 3615
    Number of Reflections(R-Free) 164
    Percent Reflections(Observed) 100.0
    R-Factor(Observed) 0.249
    R-Work 0.248
    R-Free 0.267
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 56.744
    Anisotropic B[1][1] 0.42
    Anisotropic B[1][2] 0.21
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.42
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.63
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.001
    Shell Resolution(Low) 3.078
    Number of Reflections(R-Free) 17
    Number of Reflections(R-Work) 239
    R-Factor(R-Work) 0.305
    R-Factor(R-Free) 0.238
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.264
    r_scbond_it 0.803
    r_mcangle_it 0.623
    r_mcbond_it 0.401
    r_symmetry_hbond_refined 0.35
    r_bond_refined_d 0.014
    r_angle_refined_deg 1.69
    r_dihedral_angle_1_deg 5.971
    r_dihedral_angle_2_deg 27.249
    r_dihedral_angle_3_deg 24.613
    r_dihedral_angle_4_deg 23.701
    r_chiral_restr 0.126
    r_gen_planes_refined 0.005
    r_nbd_refined 0.261
    r_nbtor_refined 0.326
    r_xyhbond_nbd_refined 0.168
    r_symmetry_vdw_refined 0.409
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1208
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MXCUBE
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 3.006
    refinement REFMAC5
    molecular replacement Phaser
    data processing SCALA version: 3.2.25
    collection/data indexing Mosflm