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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DCZ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.5
    Temperature 293.0
    Details 22% PEG 2000, 0.1 M SODIUM CITRATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 81 α = 90
    b = 81 β = 90
    c = 73.3 γ = 120
     
    Space Group
    Space Group Name:    P 31 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
    Diffrn ID 2
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Details MIRRORS
    Collection Date 2009-11-01
    Detector CCD
    Type ADSC QUANTUM 315r
    Details MIRRORS
    Collection Date 2009-07-26
     
    Diffraction Radiation
    Monochromator SI 111 CHANNEL
    Diffraction Protocol SAD
    Monochromator SI 111 CHANNEL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-4
    Wavelength List 0.979
    Site ESRF
    Beamline ID14-4
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-4
    Wavelength 0.979
    Wavelength List 0.979
    Site ESRF
    Beamline ID14-4
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.9
    Resolution(Low) 30
    Number Reflections(Observed) 6450
    Percent Possible(Observed) 74.0
    R Merge I(Observed) 0.067
    B(Isotropic) From Wilson Plot 70.0
    Redundancy 10.5
     
    High Resolution Shell Details
    Resolution(High) 2.9
    Resolution(Low) 3.0
    Percent Possible(All) 90.0
    R Merge I(Observed) 0.498
    Mean I Over Sigma(Observed) 5.2
    R-Sym I(Observed) 0.393
    Redundancy 10.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.9
    Resolution(Low) 27.18
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 6418
    Number of Reflections(R-Free) 294
    Percent Reflections(Observed) 99.8
    R-Factor(Observed) 0.206
    R-Work 0.203
    R-Free 0.26
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 62.51
    Anisotropic B[1][1] 0.22
    Anisotropic B[1][2] 0.11
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.22
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.33
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9
    Shell Resolution(Low) 2.97
    Number of Reflections(R-Free) 15
    Number of Reflections(R-Work) 425
    R-Factor(R-Work) 0.333
    R-Factor(R-Free) 0.374
    Percent Reflections(Observed) 96.49
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.086
    r_scbond_it 1.902
    r_mcangle_it 1.356
    r_mcbond_other 0.131
    r_mcbond_it 0.706
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.007
    r_chiral_restr 0.091
    r_dihedral_angle_4_deg 31.237
    r_dihedral_angle_3_deg 19.302
    r_dihedral_angle_2_deg 34.461
    r_dihedral_angle_1_deg 7.571
    r_angle_other_deg 0.935
    r_angle_refined_deg 1.705
    r_bond_other_d 0.001
    r_bond_refined_d 0.02
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 922
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution SHELXD
    Structure Refinement REFMAC 5.5.0102
     
    Software
    refinement REFMAC version: 5.5.0102
    model building SHELXD