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X-RAY DIFFRACTION
Materials and Methods page
1C1V
  •   Crystallization Hide
    Crystallization Experiments
    pH 7
    Details THROMBIN WAS PURCHASED FROM HAEMATOLOGIC TECHNOLOGIES, INC. AND ACETYL-HIRUDIN FROM BACHEM. THROMBIN WAS PREPARED AS DESCRIBED (SKRZPCZAK-JANKUN ET AL., 1991) .THROMBIN (1.0 MG/ML IN 50 MM HEPES, 50 % GLYCEROL, PH 7.0) WAS INCUBATED WITH 1.0 MM ACETYL-HIRUDIN, 1.0 MM BABIM, 1.0 MM ZN+2 FOR 1 HR AT 4 DEG C. GLYCEROL WAS REMOVED AND THE COMPLEX CONCENTRATED WITH A CENTRICON 10 (AMICON) TO 8.6 MG/ML AS DETERMINED BY THE BIORAD PROTEIN ASSAY KIT USING BOVINE SERUM ALBUMIN. CRYSTALS OF THROMBIN-ACETYL-HIRUDIN-BABIM-ZN+2 WERE GROWN IN HANGING DROPS BY VAPOR DIFFUSION AFTER STREAK SEEDING. THE DROPS WERE MADE FROM 5 MICROLITERS OF COMPLEX AND 5 MICROLITERS OF RESERVOIR SOLUTION (0.10 M TRIS, 0.50 M NACL, 22 % (BY VOLUME) PEG 4K, PH 7.00). A CO-CRYSTAL WAS SOAKED IN 30 % PEG 4K,0.50 M NACL, 0.10 M TRIS, 46 MM ZN+2, PH 7.00, SATURATED IN BABIM AND CONTAINING 2 % DMSO.
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 72.47 α = 90
    b = 72.09 β = 101.51
    c = 73.11 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 298
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS IV++
    Details MSC MIRRORS
    Collection Date 1998-02-15
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Wavelength 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 1.45
    Resolution(Low) 44.42
    Number Reflections(Observed) 22211
    Percent Possible(Observed) 62.0
    R Merge I(Observed) 0.087
    Redundancy 1.6
     
    High Resolution Shell Details
    Resolution(High) 1.98
    Resolution(Low) 2.07
    Percent Possible(All) 36.3
    R Merge I(Observed) 0.225
    Mean I Over Sigma(Observed) 1.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method DIFFERENCE FOURIER PLUS REFINEMENT
    reflnsShellList 1.98
    Resolution(Low) 7.5
    Cut-off Sigma(F) 2.75
    Number of Reflections(Observed) 15638
    Number of Reflections(R-Free) 1519
    Percent Reflections(Observed) 62.0
    R-Factor(Observed) 0.204
    R-Work 0.204
    R-Free 0.248
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.98
    Shell Resolution(Low) 2.07
    Number of Reflections(R-Free) 108
    Number of Reflections(R-Work) 1027
    R-Factor(R-Work) 0.33
    R-Factor(R-Free) 0.38
    Percent Reflections(Observed) 36.3
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    x_improper_angle_d 0.48
    x_bond_d 0.019
    x_angle_deg 4.0
    x_dihedral_angle_d 24.7
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2430
    Nucleic Acid Atoms 0
    Heterogen Atoms 28
    Solvent Atoms 263
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) BIOTEX (MSC)
    Data Reduction (data scaling) BIOTEX
    Structure Solution X-PLOR, QUANTA, INSIGHTII
    Structure Refinement X-PLOR 3.1
     
    Software
    refinement X-PLOR version: 3.1
    model building INSIGHTII
    model building QUANTA
    model building X-PLOR
    data reduction BIOTEX version: (MSC)
    data collection BIOTEX version: (MSC)