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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4KAD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Temperature 298.0
    Details 0.2M AMMONIUM ACETATE, 0.1M BIS:TRIS:HCL, PH 6.5, 25% PEG335, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 51.25 α = 90
    b = 81.2 β = 98.45
    c = 82.92 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2013-03-28
     
    Diffraction Radiation
    Diffraction Protocol single wavelength
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.075
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.7
    Resolution(Low) 50
    Number Reflections(Observed) 72142
    Percent Possible(Observed) 97.4
    R Merge I(Observed) 0.098
    Redundancy 3.6
     
    High Resolution Shell Details
    Resolution(High) 1.7
    Resolution(Low) 1.73
    Percent Possible(All) 78.8
    R Merge I(Observed) 0.423
    Redundancy 3.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.7
    Resolution(Low) 40.2
    Number of Reflections(Observed) 68385
    Number of Reflections(R-Free) 3641
    Percent Reflections(Observed) 97.5
    R-Factor(Observed) 0.16781
    R-Work 0.16518
    R-Free 0.21762
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 29.619
    Anisotropic B[1][1] -0.08
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.18
    Anisotropic B[2][2] -0.03
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.11
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7
    Shell Resolution(Low) 1.744
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 4176
    R-Factor(R-Work) 0.068
    R-Factor(R-Free) 0.128
    Percent Reflections(Observed) 80.93
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 18.921
    r_sphericity_free 40.317
    r_rigid_bond_restr 2.381
    r_gen_planes_refined 0.005
    r_chiral_restr 0.081
    r_dihedral_angle_4_deg 13.38
    r_dihedral_angle_3_deg 13.16
    r_dihedral_angle_2_deg 37.569
    r_dihedral_angle_1_deg 5.649
    r_angle_refined_deg 1.32
    r_bond_refined_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5008
    Nucleic Acid Atoms 0
    Heterogen Atoms 82
    Solvent Atoms 479
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement REFMAC 5.7.0029
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    molecular replacement Phaser
    data reduction SCALEPACK