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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DKJ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 5.6
    Temperature 294.0
    Details 10% PEG 3350, 150 mM NaCl, 50 mM sodium. For cryoprotection glycerol was added to 25% v/v, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 83.95 α = 90
    b = 83.95 β = 90
    c = 173.84 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Details BENT MIRRORS
    Collection Date 2010-12-05
     
    Diffraction Radiation
    Monochromator DOUBLE CRYSTAL MONOCHROMATOR
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I02
    Wavelength 0.97949
    Site DIAMOND
    Beamline I02
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.15
    Resolution(Low) 40
    Number Reflections(All) 34324
    Number Reflections(Observed) 34324
    Percent Possible(Observed) 99.3
    R Merge I(Observed) 0.078
    B(Isotropic) From Wilson Plot 33.4
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 2.15
    Resolution(Low) 2.27
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.31
    Mean I Over Sigma(Observed) 2.5
    R-Sym I(Observed) 0.31
    Redundancy 4.0
    Number Unique Reflections(All) 4957
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.15
    Resolution(Low) 38.6
    Number of Reflections(all) 34274
    Number of Reflections(Observed) 34274
    Number of Reflections(R-Free) 1729
    Percent Reflections(Observed) 98.96
    R-Factor(All) 0.17832
    R-Factor(Observed) 0.17832
    R-Work 0.17632
    R-Free 0.21631
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.15
    Shell Resolution(Low) 2.206
    Number of Reflections(Observed) 2486
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2348
    R-Factor(R-Work) 0.203
    R-Factor(R-Free) 0.288
    Percent Reflections(Observed) 99.92
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_nbd_refined 0.192
    r_gen_planes_other 0.007
    r_gen_planes_refined 0.007
    r_dihedral_angle_4_deg 15.209
    r_dihedral_angle_3_deg 15.063
    r_dihedral_angle_2_deg 38.254
    r_dihedral_angle_1_deg 6.16
    r_angle_other_deg 3.966
    r_angle_refined_deg 1.253
    r_bond_other_d 0.0
    r_bond_refined_d 0.01
    r_nbd_other 0.232
    r_nbtor_refined 0.181
    r_nbtor_other 0.108
    r_xyhbond_nbd_refined 0.137
    r_symmetry_vdw_refined 0.079
    r_symmetry_vdw_other 0.38
    r_symmetry_hbond_refined 0.084
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3199
    Nucleic Acid Atoms 570
    Heterogen Atoms 32
    Solvent Atoms 267
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution MOLREP, CHAINSAW, REFMAC, ARP/WARP
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019
    model building ARP/WARP
    model building REFMAC
    model building CHAINSAW
    model building MOLREP
    data collection ADSC version: Quantum