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An Information Portal to 110790 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1ZVW
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8
    Temperature 291.5
    Details PEG 6K, MgSO4, cacodylic acid, benzamidine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.5K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 80.42 α = 90
    b = 82.08 β = 90
    c = 118.87 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 113
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU
    Collection Date 2004-01-15
     
    Diffraction Radiation
    Monochromator Ni Filter
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RUH3R
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.3
    Resolution(Low) 25
    Number Reflections(All) 35678
    Number Reflections(Observed) 35653
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.097
    B(Isotropic) From Wilson Plot 43.0
    Redundancy 9.0
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.38
    Percent Possible(All) 99.4
    R Merge I(Observed) 0.67
    Mean I Over Sigma(Observed) 2.74
    Number Unique Reflections(All) 3465
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.3
    Resolution(Low) 25.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 35591
    Number of Reflections(Observed) 33839
    Number of Reflections(R-Free) 1784
    Percent Reflections(Observed) 99.83
    R-Factor(Observed) 0.197
    R-Work 0.194
    R-Free 0.255
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 36.104
    Anisotropic B[1][1] -0.36
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.33
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.69
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.299
    Shell Resolution(Low) 2.358
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2436
    R-Factor(R-Work) 0.241
    R-Factor(R-Free) 0.321
    R-Free Error 0.014
    Percent Reflections(Observed) 99.38
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_mcbond_it 1.29
    c_improper_angle_d 4.8
    c_dihedral_angle_d 24.9
    c_angle_deg 3.0
    c_angle_d 0.082
     
    Coordinate Error
    Luzzati ESD(Observed) 0.24
    Luzzati Sigma A(Observed) 0.18
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.25
    Luzzati Sigma A(R-Free Set) 0.21
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4876
    Nucleic Acid Atoms 0
    Heterogen Atoms 33
    Solvent Atoms 277
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MOLREP
    Structure Refinement REFMAC 5
     
    Software
    data extraction pdb_extract version: 1.601
    refinement REFMAC5
    molecular replacement MOLREP
    data processing HKL