POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4GVU
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5
    Temperature 293.0
    Details 0.01 M sodium acetate pH 5.0, 0.42 M sodium sulfate, hanging drop, lyngbyastatin 7 dissolved in methanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 53.4 α = 90
    b = 57.42 β = 90
    c = 74.33 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector AREA DETECTOR
    Type ADSC QUANTUM 210
    Details Rh coated toroidal focusing mirror
    Collection Date 2008-06-27
     
    Diffraction Radiation
    Monochromator Si(111) channel cut
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X6A
    Wavelength List 0.9537
    Site NSLS
    Beamline X6A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.55
    Resolution(Low) 30
    Number Reflections(All) 33573
    Number Reflections(Observed) 33573
    Percent Possible(Observed) 99.6
    R Merge I(Observed) 0.044
    B(Isotropic) From Wilson Plot 20.6
    Redundancy 7.7
     
    High Resolution Shell Details
    Resolution(High) 1.55
    Resolution(Low) 1.56
    Percent Possible(All) 84.0
    R Merge I(Observed) 0.55
    Mean I Over Sigma(Observed) 2.0
    Redundancy 4.9
    Number Unique Reflections(All) 699
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.55
    Resolution(Low) 28.71
    Number of Reflections(Observed) 31822
    Number of Reflections(R-Free) 1696
    Percent Reflections(Observed) 99.89
    R-Factor(Observed) 0.17754
    R-Work 0.17606
    R-Free 0.2062
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 24.39
    Anisotropic B[1][1] 2.14
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.97
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.17
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.555
    Shell Resolution(Low) 1.595
    Number of Reflections(R-Free) 107
    Number of Reflections(R-Work) 2141
    R-Factor(R-Work) 0.272
    R-Factor(R-Free) 0.33
    Percent Reflections(Observed) 99.16
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.008
    r_chiral_restr 0.149
    r_dihedral_angle_4_deg 20.521
    r_dihedral_angle_3_deg 12.535
    r_dihedral_angle_2_deg 36.827
    r_dihedral_angle_1_deg 6.402
    r_angle_refined_deg 1.709
    r_bond_refined_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1890
    Nucleic Acid Atoms 0
    Heterogen Atoms 6
    Solvent Atoms 243
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DCS_X6A
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.6.0117
     
    Software
    refinement REFMAC version: 5.6.0117
    model building MOLREP
    data collection DCS_X6A