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X-RAY DIFFRACTION
Materials and Methods page
3VAF
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 277.0
    Details 1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 164.3 α = 90
    b = 36.98 β = 125.67
    c = 99.43 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2005-11-02
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 0.960
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -1.0
    Resolution(High) 2.49
    Resolution(Low) 50
    Number Reflections(Observed) 17441
    Percent Possible(Observed) 99.3
    R Merge I(Observed) 0.134
    Redundancy 6.6
     
    High Resolution Shell Details
    Resolution(High) 2.49
    Resolution(Low) 2.58
    Percent Possible(All) 99.3
    R Merge I(Observed) 0.455
    Redundancy 4.7
    Number Unique Reflections(All) 1612
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.49
    Resolution(Low) 20.51
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 17997
    Number of Reflections(Observed) 16380
    Number of Reflections(R-Free) 1617
    Percent Reflections(Observed) 93.5
    R-Factor(Observed) 0.2361
    R-Work 0.2305
    R-Free 0.2886
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 35.2124
    Anisotropic B[1][1] -0.64
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.5
    Anisotropic B[2][2] 0.23
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.486
    Shell Resolution(Low) 2.55
    Number of Reflections(R-Free) 96
    Number of Reflections(R-Work) 963
    R-Factor(R-Work) 0.371
    R-Factor(R-Free) 0.459
    Percent Reflections(Observed) 84.79
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.793
    r_nbd_refined 0.216
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.004
    r_chiral_restr 0.096
    r_dihedral_angle_4_deg 16.232
    r_dihedral_angle_3_deg 16.179
    r_dihedral_angle_2_deg 35.579
    r_dihedral_angle_1_deg 6.179
    r_angle_other_deg 1.093
    r_angle_refined_deg 1.401
    r_bond_other_d 0.005
    r_bond_refined_d 0.011
    r_nbd_other 0.196
    r_nbtor_refined 0.188
    r_nbtor_other 0.086
    r_xyhbond_nbd_refined 0.15
    r_xyhbond_nbd_other 0.041
    r_symmetry_vdw_refined 0.194
    r_symmetry_vdw_other 0.174
    r_symmetry_hbond_refined 0.16
    r_mcbond_it 0.509
    r_mcbond_other 0.082
    r_mcangle_it 0.633
    r_scbond_it 1.149
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2675
    Nucleic Acid Atoms 226
    Heterogen Atoms 87
    Solvent Atoms 119
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5 version: 5.2.0019
    data reduction SCALEPACK
    data collection DENZO