POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DXJ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5
    Temperature 291.0
    Details 12.5 mg/mL protein in 250 uM inhibitor, 250 uM IPP, 1 mM magnesium chloride, mother liquor: 100 mM sodium acetate, pH 4.6-5.2, 200 mM ammonium sulfate, 2-10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 103.22 α = 90
    b = 103.22 β = 90
    c = 386.66 γ = 120
     
    Space Group
    Space Group Name:    P 61 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210
    Collection Date 2011-12-06
     
    Diffraction Radiation
    Monochromator Si(111) channel cut
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X6A
    Wavelength List 0.979
    Site NSLS
    Beamline X6A
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.35
    Resolution(Low) 89.39
    Number Reflections(Observed) 49874
    Percent Possible(Observed) 96.0
    R Merge I(Observed) 0.09
    Redundancy 9.1
     
    High Resolution Shell Details
    Resolution(High) 2.35
    Resolution(Low) 2.39
    Percent Possible(All) 93.7
    R Merge I(Observed) 0.52
    Redundancy 6.8
    Number Unique Reflections(All) 2346
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 2.35
    Resolution(Low) 38.722
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 49345
    Number of Reflections(R-Free) 2519
    Percent Reflections(Observed) 95.23
    R-Factor(Observed) 0.2228
    R-Work 0.2195
    R-Free 0.2853
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 40.287
    Anisotropic B[1][1] 1.12
    Anisotropic B[1][2] 0.56
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.12
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.69
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.35
    Shell Resolution(Low) 2.48
    Number of Reflections(R-Free) 378
    Number of Reflections(R-Work) 6754
    R-Factor(R-Work) 0.251
    R-Factor(R-Free) 0.334
    Percent Reflections(Observed) 97.01
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.131
    r_scbond_it 1.341
    r_mcangle_it 0.793
    r_mcbond_it 0.404
    r_gen_planes_refined 0.005
    r_chiral_restr 0.089
    r_dihedral_angle_4_deg 19.456
    r_dihedral_angle_3_deg 17.148
    r_dihedral_angle_2_deg 40.916
    r_dihedral_angle_1_deg 4.773
    r_angle_refined_deg 1.208
    r_bond_refined_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 8673
    Nucleic Acid Atoms 0
    Heterogen Atoms 152
    Solvent Atoms 161
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution REFMAC
    Structure Refinement REFMAC 5.5.0109
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    data reduction SCALEPACK