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X-RAY DIFFRACTION
Materials and Methods page
3VMX
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7
    Temperature 283.0
    Details 2% V/V TACSIMATE (PH 7.0), 0.1M IMIDAZOLE (PH 7.0), 8% W/V PEG 3350, 5% V/V 2-PROPANOL (PEGRX-2 # 26, HAMPTOM), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 40.16 α = 90
    b = 54.01 β = 90
    c = 81.44 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 200
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX225HE
    Collection Date 2009-11-22
     
    Diffraction Radiation
    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) 1.45
    Resolution(Low) 50
    Number Reflections(Observed) 232980
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.056
    Redundancy 7.2
     
    High Resolution Shell Details
    Resolution(High) 1.45
    Resolution(Low) 1.48
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.44
    Mean I Over Sigma(Observed) 4.741
    R-Sym I(Observed) 0.44
    Redundancy 7.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.45
    Resolution(Low) 45.01
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 32168
    Number of Reflections(R-Free) 1630
    Percent Reflections(Observed) 99.7
    R-Factor(Observed) 0.181
    R-Work 0.179
    R-Free 0.214
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 19.72
    Anisotropic B[1][1] 0.07
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.13
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.2
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.45
    Shell Resolution(Low) 1.49
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2228
    R-Factor(R-Work) 0.197
    R-Factor(R-Free) 0.247
    Percent Reflections(Observed) 98.95
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 6.174
    r_scbond_it 3.896
    r_mcangle_it 2.39
    r_mcbond_it 1.43
    r_gen_planes_refined 0.011
    r_chiral_restr 0.175
    r_dihedral_angle_4_deg 19.285
    r_dihedral_angle_3_deg 16.452
    r_dihedral_angle_2_deg 44.311
    r_dihedral_angle_1_deg 4.444
    r_angle_refined_deg 2.483
    r_bond_refined_d 0.027
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1560
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 222
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0102
     
    Software
    refinement REFMAC version: 5.5.0102
    model building PHASER