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An Information Portal to 110790 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4IVZ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 289.0
    Details 0.1 M SPG buffer, 25 % w/v PEG 1500, 10 uM Spermidine , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 47.54 α = 90
    b = 146.7 β = 93.21
    c = 47.79 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 315r
    Collection Date 2012-10-31
     
    Diffraction Radiation
    Monochromator Si(111) double crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I04
    Wavelength List 0.9795
    Site DIAMOND
    Beamline I04
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 3.1
    Resolution(Low) 146.81
    Number Reflections(All) 11888
    Number Reflections(Observed) 11810
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.111
    Redundancy 3.5
     
    High Resolution Shell Details
    Resolution(High) 3.1
    Resolution(Low) 3.31
    Percent Possible(All) 99.6
    R Merge I(Observed) 0.666
    Mean I Over Sigma(Observed) 1.8
    Redundancy 3.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.1
    Resolution(Low) 34.63
    Number of Reflections(all) 11888
    Number of Reflections(Observed) 11333
    Number of Reflections(R-Free) 548
    Percent Reflections(Observed) 98.61
    R-Factor(Observed) 0.17194
    R-Work 0.16987
    R-Free 0.21478
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 73.261
    Anisotropic B[1][1] -0.86
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.27
    Anisotropic B[2][2] 1.5
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.64
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.087
    Shell Resolution(Low) 3.167
    Number of Reflections(R-Free) 40
    Number of Reflections(R-Work) 753
    R-Factor(R-Work) 0.151
    R-Factor(R-Free) 0.182
    Percent Reflections(Observed) 86.29
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.008
    r_chiral_restr 0.102
    r_dihedral_angle_4_deg 20.344
    r_dihedral_angle_3_deg 22.384
    r_dihedral_angle_2_deg 35.066
    r_dihedral_angle_1_deg 7.331
    r_angle_refined_deg 1.708
    r_bond_refined_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2482
    Nucleic Acid Atoms 1546
    Heterogen Atoms 0
    Solvent Atoms 2
     
     
  •   Software and Computing Hide
    Computing
    Data Collection GDA
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) Aimless
    Structure Solution PHASER
    Structure Refinement REFMAC 5.7.0029
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    molecular replacement Phaser version: 2.5.1
    data reduction AIMLESS version: 0.1.26
    data collection Mosflm