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An Information Portal to 111558 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3QUD
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 293.0
    Details 100 mM MES, 20-30% PEG 4000, 50mM n-BOG, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 66.78 α = 90
    b = 73.37 β = 90
    c = 79.59 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 90
     
    Diffraction Detector
    Detector CCD
    Type PSI PILATUS 6M
    Details Dynamic bendable mirror
    Collection Date 2011-02-15
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X10SA
    Wavelength List 1.000000
    Site SLS
    Beamline X10SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2
    Resolution(Low) 45
    Number Reflections(All) 27068
    Number Reflections(Observed) 26734
    Percent Possible(Observed) 98.8
    R Merge I(Observed) 0.057
    B(Isotropic) From Wilson Plot 35.687
    Redundancy 4.13
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.1
    Percent Possible(All) 99.4
    R Merge I(Observed) 0.434
    Mean I Over Sigma(Observed) 3.7
    Redundancy 4.3
    Number Unique Reflections(All) 3618
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 41.96
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 26733
    Number of Reflections(Observed) 26733
    Number of Reflections(R-Free) 936
    Percent Reflections(Observed) 100.0
    R-Factor(Observed) 0.2335
    R-Work 0.2318
    R-Free 0.278
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 28.8361
    Anisotropic B[1][1] -0.1
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.1
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.052
    Number of Reflections(R-Free) 68
    Number of Reflections(R-Work) 1875
    R-Factor(R-Work) 0.307
    R-Factor(R-Free) 0.356
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.276
    r_scbond_it 1.984
    r_mcangle_it 1.427
    r_mcbond_it 0.768
    r_gen_planes_refined 0.006
    r_chiral_restr 0.088
    r_dihedral_angle_4_deg 20.981
    r_dihedral_angle_3_deg 16.697
    r_dihedral_angle_2_deg 36.779
    r_dihedral_angle_1_deg 5.622
    r_angle_refined_deg 1.294
    r_bond_refined_d 0.012
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2772
    Nucleic Acid Atoms 0
    Heterogen Atoms 62
    Solvent Atoms 103
     
     
  •   Software and Computing Hide
    Computing
    Data Collection XDS
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0102
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5 version: 5.5.0102
    molecular replacement Phaser version: 2.1.4
    data processing Xscale