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An Information Portal to 109093 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4GAE
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    Temperature 298.0
    Details The protein solution containing 10 mg/mL PfDXR, 2 mM inhibitor, 3 mM NADPH, 2 mM MnCl2, 2 mM DTT, 50 mM Tris, pH 7.8 was mixed with an equal volume of the reservoir solution of 0.1 M Tris, pH 8.0, 20% PEG 3350, 0.3 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 51.36 α = 90
    b = 77.28 β = 91.5
    c = 109.41 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 93
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS HTC
    Details Mirrors
    Collection Date 2011-08-26
     
    Diffraction Radiation
    Monochromator MIRROR
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU FR-E+ SUPERBRIGHT
    Wavelength List 1.54178
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.3
    Resolution(Low) 51.34
    Number Reflections(Observed) 34047
    Percent Possible(Observed) 89.2
    R Merge I(Observed) 0.064
    B(Isotropic) From Wilson Plot 32.94
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.42
    Percent Possible(All) 64.8
    R Merge I(Observed) 0.125
    Mean I Over Sigma(Observed) 6.9
    Redundancy 3.2
    Number Unique Reflections(All) 3590
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.3
    Resolution(Low) 44.64
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 34035
    Number of Reflections(R-Free) 1698
    Percent Reflections(Observed) 89.0
    R-Factor(Observed) 0.23
    R-Work 0.23
    R-Free 0.273
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 37.3
    Anisotropic B[1][1] -3.79
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -5.39
    Anisotropic B[2][2] -0.92
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 4.71
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.38
    Number of Reflections(Observed) 2321
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2191
    R-Factor(R-Work) 0.247
    R-Factor(R-Free) 0.32
    R-Free Error 0.028
    Percent Reflections(Observed) 61.5
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 3.05
    c_scbond_it 2.12
    c_mcangle_it 2.24
    c_mcbond_it 1.36
    c_improper_angle_d 0.88
    c_dihedral_angle_d 21.0
    c_angle_deg 1.3
    c_bond_d 0.007
     
    Coordinate Error
    Luzzati ESD(Observed) 0.26
    Luzzati Sigma A(Observed) 0.24
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.33
    Luzzati Sigma A(R-Free Set) 0.34
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6600
    Nucleic Acid Atoms 0
    Heterogen Atoms 193
    Solvent Atoms 138
     
     
  •   Software and Computing Hide
    Computing
    Data Collection StructureStudio
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution Phaser
    Structure Refinement CNS 1.3
     
    Software
    refinement CNS version: 1.3
    model building Phaser
    data collection StructureStudio