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X-RAY DIFFRACTION
Materials and Methods page
3VMY
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 283.0
    Details 0.1M KCL, 0.05M TRIS-HCL PH8.0, 0.1M SODIUM MALONATE, 30% PEG 1,000, 5MM DTT, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 40.17 α = 90
    b = 54.07 β = 90
    c = 81.54 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 RAYONIX MX225HE
    Collection Date 2010-05-23
     
    Diffraction Radiation
    Monochromator SI 111
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL44XU
    Wavelength 0.9000
    Site SPRING-8
    Beamline BL44XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.47
    Resolution(Low) 50
    Number Reflections(Observed) 30985
    Percent Possible(Observed) 99.6
    R Merge I(Observed) 0.07
    Redundancy 7.2
     
    High Resolution Shell Details
    Resolution(High) 1.47
    Resolution(Low) 1.5
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.495
    Mean I Over Sigma(Observed) 4.043
    R-Sym I(Observed) 0.495
    Redundancy 7.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.47
    Resolution(Low) 29.98
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 30921
    Number of Reflections(R-Free) 1560
    Percent Reflections(Observed) 99.5
    R-Factor(Observed) 0.2
    R-Work 0.198
    R-Free 0.234
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 22.51
    Anisotropic B[1][1] 0.07
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.04
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.03
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.47
    Shell Resolution(Low) 1.5
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2072
    R-Factor(R-Work) 0.21
    R-Factor(R-Free) 0.249
    Percent Reflections(Observed) 97.29
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 5.477
    r_scbond_it 3.543
    r_mcangle_it 2.127
    r_mcbond_it 1.335
    r_gen_planes_refined 0.01
    r_chiral_restr 0.15
    r_dihedral_angle_4_deg 19.636
    r_dihedral_angle_3_deg 15.034
    r_dihedral_angle_2_deg 41.66
    r_dihedral_angle_1_deg 4.246
    r_angle_refined_deg 2.165
    r_bond_refined_d 0.023
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1558
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 237
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL
    Data Reduction (data scaling) HKL
    Structure Solution REFMAC 5.5.0102
    Structure Refinement REFMAC 5.5.0102
     
    Software
    refinement REFMAC version: 5.5.0102
    model building REFMAC version: 5.5.0102