POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3VX3
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5
    Temperature 293.0
    Details 1.0M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 66.24 α = 90
    b = 137.69 β = 90
    c = 150.82 γ = 90
     
    Space Group
    Space Group Name:    I 2 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 95
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-225
    Collection Date 2009-12-03
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL41XU
    Wavelength List 1.0000
    Site SPRING-8
    Beamline BL41XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.1
    Resolution(Low) 50
    Number Reflections(Observed) 40492
    Percent Possible(Observed) 99.8
    Redundancy 7.1
     
    High Resolution Shell Details
    Resolution(High) 2.1
    Resolution(Low) 2.18
    Percent Possible(All) 100.0
    Mean I Over Sigma(Observed) 3.6
    R-Sym I(Observed) 0.529
    Redundancy 6.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.1
    Resolution(Low) 40.22
    Number of Reflections(Observed) 38324
    Number of Reflections(R-Free) 2010
    Percent Reflections(Observed) 99.45
    R-Factor(Observed) 0.19485
    R-Work 0.19362
    R-Free 0.21845
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 39.133
    Anisotropic B[1][1] -1.98
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.22
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.77
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1
    Shell Resolution(Low) 2.156
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2766
    R-Factor(R-Work) 0.268
    R-Factor(R-Free) 0.305
    Percent Reflections(Observed) 99.12
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.449
    r_scbond_it 2.101
    r_mcangle_it 1.286
    r_mcbond_it 0.699
    r_gen_planes_refined 0.007
    r_chiral_restr 0.092
    r_dihedral_angle_4_deg 17.933
    r_dihedral_angle_3_deg 14.838
    r_dihedral_angle_2_deg 33.251
    r_dihedral_angle_1_deg 5.979
    r_angle_refined_deg 1.497
    r_bond_refined_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3678
    Nucleic Acid Atoms 0
    Heterogen Atoms 78
    Solvent Atoms 175
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution SOLVE
    Structure Refinement REFMAC 5.5.0109
     
    Software
    refinement REFMAC version: 5.5.0109
    model building SOLVE