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X-RAY DIFFRACTION
Materials and Methods page
1PKD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.4
    Temperature 277.0
    Details 1.25M (NH4)2SO4, 0.8M KCl, 100mM HEPES, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 73.62 α = 90
    b = 134.57 β = 90
    c = 147.97 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-1
    Wavelength List 0.934
    Site ESRF
    Beamline ID14-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.3
    Resolution(Low) 100
    Number Reflections(All) 65518
    Number Reflections(Observed) 57525
    Percent Possible(Observed) 87.8
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.38
    Percent Possible(All) 80.8
    Mean I Over Sigma(Observed) 2.6
    R-Sym I(Observed) 0.331
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.3
    Resolution(Low) 100.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 57525
    Number of Reflections(Observed) 54590
    Number of Reflections(R-Free) 2904
    Percent Reflections(Observed) 87.03
    R-Factor(All) 0.21818
    R-Factor(Observed) 0.21818
    R-Work 0.2155
    R-Free 0.26831
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 42.484
    Anisotropic B[1][1] -0.76
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.81
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.05
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.36
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 3636
    R-Factor(R-Work) 0.268
    R-Factor(R-Free) 0.343
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.079
    r_bond_refined_d 0.009
    r_angle_refined_deg 1.54
    r_dihedral_angle_1_deg 5.824
    r_chiral_restr 0.095
    r_gen_planes_refined 0.004
    r_nbd_refined 0.218
    r_xyhbond_nbd_refined 0.162
    r_symmetry_vdw_refined 0.311
    r_symmetry_hbond_refined 0.215
    r_mcbond_it 0.844
    r_mcangle_it 1.598
    r_scbond_it 1.765
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 8942
    Nucleic Acid Atoms 0
    Heterogen Atoms 72
    Solvent Atoms 402
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) CCP4 (SCALA)
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.1.19
     
    Software
    refinement REFMAC version: 5.1.19