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An Information Portal to 106082 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3M6K
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5
    Temperature 303.0
    Details 0.1 M phosphate-citrate pH 5, 0.2 M NaCl, 16% PEG 8000, 1M Guanidium hydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 303K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 70.09 α = 90
    b = 70.09 β = 90
    c = 349.63 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-225
    Collection Date 2008-04-23
    Detector CCD
    Type RAYONIX MX-225
    Details beryllium lenses
    Collection Date 2008-04-23
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
    Monochromator silicon
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-D
    Wavelength List 0.97915
    Site APS
    Beamline 21-ID-D
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-G
    Wavelength List 0.97872
    Site APS
    Beamline 21-ID-G
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.6
    Resolution(Low) 29.5
    Number Reflections(All) 28160
    Number Reflections(Observed) 28151
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.079
    B(Isotropic) From Wilson Plot 42.1
    Redundancy 8.1
     
    High Resolution Shell Details
    Resolution(High) 2.6
    Resolution(Low) 2.72
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.572
    Mean I Over Sigma(Observed) 3.2
    R-Sym I(Observed) 0.522
    Redundancy 6.0
    Number Unique Reflections(All) 3331
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.6
    Resolution(Low) 29.14
    Number of Reflections(all) 28151
    Number of Reflections(Observed) 26710
    Number of Reflections(R-Free) 1438
    Percent Reflections(Observed) 99.96
    R-Factor(All) 0.24371
    R-Factor(Observed) 0.24371
    R-Work 0.24132
    R-Free 0.28883
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 55.918
    Anisotropic B[1][1] 2.02
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.02
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -4.04
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6
    Shell Resolution(Low) 2.667
    Number of Reflections(Observed) 1897
    Number of Reflections(R-Free) 93
    Number of Reflections(R-Work) 1897
    R-Factor(R-Work) 0.366
    R-Factor(R-Free) 0.451
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.464
    r_scbond_it 0.968
    r_mcangle_it 0.58
    r_mcbond_other 0.086
    r_mcbond_it 0.522
    r_symmetry_hbond_refined 0.16
    r_symmetry_vdw_other 0.263
    r_symmetry_vdw_refined 0.202
    r_xyhbond_nbd_refined 0.15
    r_nbtor_other 0.085
    r_nbtor_refined 0.179
    r_nbd_other 0.185
    r_bond_refined_d 0.011
    r_bond_other_d 0.002
    r_angle_refined_deg 1.203
    r_angle_other_deg 0.89
    r_dihedral_angle_1_deg 5.538
    r_dihedral_angle_2_deg 34.326
    r_dihedral_angle_3_deg 17.444
    r_dihedral_angle_4_deg 18.828
    r_chiral_restr 0.067
    r_gen_planes_refined 0.003
    r_gen_planes_other 0.001
    r_nbd_refined 0.226
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5967
    Nucleic Acid Atoms 0
    Heterogen Atoms 15
    Solvent Atoms 30
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MD2-microdiffractometer
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution SHARP
    Structure Refinement REFMAC 5.2.0019
     
    Software
    refinement REFMAC version: 5.2.0019
    model building SHARP
    data collection MD2-microdiffractometer