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An Information Portal to 106082 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DZ0
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8
    Temperature 298.0
    Details 50 mM Tris, 5 mM calcium chloride, 50 mM sodium chloride, 10% PEG 3350, 350 M cupric chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 180.43 α = 90
    b = 180.43 β = 90
    c = 180.43 γ = 90
     
    Space Group
    Space Group Name:    F 4 3 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 325 mm CCD
    Collection Date 2011-07-23
     
    Diffraction Radiation
    Monochromator Rh coated flat mirror, toroidal focusing mirror
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL9-2
    Wavelength List 0.98
    Site SSRL
    Beamline BL9-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 3.0
    Observed Criterion Sigma(I) 3.0
    Resolution(High) 2.5
    Resolution(Low) 104.17
    Number Reflections(All) 9200
    Number Reflections(Observed) 9200
    Percent Possible(Observed) 100.0
    Redundancy 20.3
     
    High Resolution Shell Details
    Resolution(High) 2.5
    Resolution(Low) 2.64
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.405
    Mean I Over Sigma(Observed) 1.9
    R-Sym I(Observed) 0.405
    Redundancy 20.9
    Number Unique Reflections(All) 1294
     
     
  •   Refinement Hide
    Refinement Statistics
    reflnsShellList 2.5
    Resolution(Low) 36.84
    Number of Reflections(Observed) 8548
    Number of Reflections(R-Free) 649
    Percent Reflections(Observed) 99.98
    R-Factor(Observed) 0.22945
    R-Work 0.2243
    R-Free 0.29992
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 38.57
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5
    Shell Resolution(Low) 2.565
    Number of Reflections(R-Free) 36
    Number of Reflections(R-Work) 611
    R-Factor(R-Work) 0.294
    R-Factor(R-Free) 0.353
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.737
    r_scbond_it 1.14
    r_mcangle_it 0.771
    r_mcbond_it 0.417
    r_nbd_refined 0.181
    r_gen_planes_refined 0.003
    r_chiral_restr 0.074
    r_dihedral_angle_4_deg 18.69
    r_dihedral_angle_3_deg 15.184
    r_dihedral_angle_2_deg 39.989
    r_dihedral_angle_1_deg 4.887
    r_angle_refined_deg 0.953
    r_bond_refined_d 0.007
    r_nbtor_refined 0.29
    r_xyhbond_nbd_refined 0.121
    r_metal_ion_refined 0.022
    r_symmetry_vdw_refined 0.173
    r_symmetry_hbond_refined 0.149
    r_symmetry_metal_ion_refined 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1410
    Nucleic Acid Atoms 0
    Heterogen Atoms 27
    Solvent Atoms 51
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BluIce
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.2.0005
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    molecular replacement MOLREP
    data reduction SCALA version: 3.3.15
    data collection Mosflm