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X-RAY DIFFRACTION
Materials and Methods page
3ZDT
  •   Crystallization Hide
    Crystallization Experiments
    pH 8.5
    Details 14% PEG4K, 200 MM MGCL2, 100 MM TRIS PH 8.5, 10 MM TCEP
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 41.57 α = 90
    b = 175.53 β = 93.94
    c = 60.03 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL (PILATUS)
    Type DECTRIS
    Collection Date 2010-11-18
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-4
    Wavelength 1.07214
    Site ESRF
    Beamline ID14-4
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 3.15
    Resolution(Low) 50
    Number Reflections(Observed) 14023
    Percent Possible(Observed) 99.6
    R Merge I(Observed) 0.1
    Redundancy 3.77
     
    High Resolution Shell Details
    Resolution(High) 3.15
    Resolution(Low) 3.34
    Percent Possible(All) 99.6
    R Merge I(Observed) 0.52
    Mean I Over Sigma(Observed) 2.6
    Redundancy 3.76
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.15
    Resolution(Low) 43.88
    Number of Reflections(Observed) 14023
    Number of Reflections(R-Free) 739
    Percent Reflections(Observed) 99.58
    R-Factor(Observed) 0.21745
    R-Work 0.21427
    R-Free 0.27822
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 79.6
    Anisotropic B[1][1] -0.26
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.05
    Anisotropic B[2][2] 0.27
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.02
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.151
    Shell Resolution(Low) 3.232
    Number of Reflections(R-Free) 54
    Number of Reflections(R-Work) 1020
    R-Factor(R-Work) 0.326
    R-Factor(R-Free) 0.405
    Percent Reflections(Observed) 97.55
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.519
    r_scbond_it 1.425
    r_mcangle_it 1.128
    r_mcbond_it 0.583
    r_gen_planes_refined 0.007
    r_chiral_restr 0.107
    r_dihedral_angle_4_deg 11.278
    r_dihedral_angle_3_deg 10.446
    r_dihedral_angle_2_deg 14.347
    r_dihedral_angle_1_deg 4.82
    r_angle_refined_deg 1.609
    r_bond_refined_d 0.019
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5185
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 7
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0109
     
    Software
    refinement REFMAC version: 5.5.0109
    model building PHASER