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X-RAY DIFFRACTION
Materials and Methods page
3VMZ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 283.0
    Details 0.1M KCL, 0.05 M TRIS-HCL PH8.0, 0.1M SODIUM MALONATE, 30% PEG 1000, 5MM H2O2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 40.31 α = 90
    b = 54.15 β = 90
    c = 81.88 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) 1.55
    Resolution(Low) 50
    Number Reflections(Observed) 26858
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.075
    Redundancy 12.3
     
    High Resolution Shell Details
    Resolution(High) 1.55
    Resolution(Low) 1.58
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.48
    Mean I Over Sigma(Observed) 4.675
    R-Sym I(Observed) 0.48
    Redundancy 7.4
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.55
    Resolution(Low) 40.94
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 26774
    Number of Reflections(R-Free) 1346
    Percent Reflections(Observed) 99.7
    R-Factor(Observed) 0.195
    R-Work 0.193
    R-Free 0.233
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 23.77
    Anisotropic B[1][1] 0.09
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.08
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.17
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.55
    Shell Resolution(Low) 1.59
    Number of Reflections(R-Free) 96
    Number of Reflections(R-Work) 1774
    R-Factor(R-Work) 0.231
    R-Factor(R-Free) 0.269
    Percent Reflections(Observed) 97.65
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 6.164
    r_scbond_it 3.749
    r_mcangle_it 2.404
    r_mcbond_it 1.512
    r_gen_planes_refined 0.01
    r_chiral_restr 0.175
    r_dihedral_angle_4_deg 19.931
    r_dihedral_angle_3_deg 15.855
    r_dihedral_angle_2_deg 42.799
    r_dihedral_angle_1_deg 4.142
    r_angle_refined_deg 2.36
    r_bond_refined_d 0.025
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1556
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 225
     
     
  •   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