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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3DNF
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 291.0
    Details 10 % (w/w) PEG 8000, 0,1 M Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 60.37 α = 90
    b = 87.76 β = 95.13
    c = 72.4 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 CCD
    Type MARMOSAIC 225 mm CCD
    Details mirrors
    Collection Date 2007-07-01
     
    Diffraction Radiation
    Monochromator Si 111 CHANNEL
    Diffraction Protocol MAD
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X10SA
    Wavelength List 0.983
    Site SLS
    Beamline X10SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.65
    Resolution(Low) 9.9
    Number Reflections(Observed) 78765
    Percent Possible(Observed) 87.2
    Redundancy 3.571
     
    High Resolution Shell Details
    Resolution(High) 1.65
    Resolution(Low) 1.7
    Percent Possible(All) 53.4
    Mean I Over Sigma(Observed) 3.29
    R-Sym I(Observed) 0.321
    Redundancy 2.356
    Number Unique Reflections(All) 9714
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 1.65
    Resolution(Low) 9.9
    Number of Reflections(Observed) 77992
    Number of Reflections(R-Free) 4120
    Percent Reflections(Observed) 91.35
    R-Factor(Observed) 0.19429
    R-Work 0.1926
    R-Free 0.22605
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 35.247
    Anisotropic B[1][1] 0.68
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.7
    Anisotropic B[2][2] 0.1
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.66
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.65
    Shell Resolution(Low) 1.692
    Number of Reflections(Observed) 3498
    Number of Reflections(R-Free) 222
    Number of Reflections(R-Work) 3498
    R-Factor(R-Work) 0.289
    R-Factor(R-Free) 0.344
    Percent Reflections(Observed) 57.04
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.488
    r_scbond_it 2.28
    r_mcangle_it 1.329
    r_mcbond_it 0.883
    r_nbd_refined 0.203
    r_gen_planes_refined 0.006
    r_chiral_restr 0.249
    r_dihedral_angle_4_deg 16.739
    r_dihedral_angle_3_deg 14.371
    r_dihedral_angle_2_deg 35.011
    r_dihedral_angle_1_deg 5.409
    r_angle_refined_deg 1.455
    r_bond_refined_d 0.017
    r_nbtor_refined 0.303
    r_xyhbond_nbd_refined 0.21
    r_symmetry_vdw_refined 0.193
    r_symmetry_hbond_refined 0.176
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4412
    Nucleic Acid Atoms 0
    Heterogen Atoms 26
    Solvent Atoms 561
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution SHARP
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019