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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3VDM
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8
    Temperature 298.0
    Details 100 mM Tris-HCl, pH 8.0, 20-35% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 85.24 α = 90
    b = 48.56 β = 91.88
    c = 123.05 γ = 90
     
    Space Group
    Space Group Name:    P 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2011-07-18
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.9479
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.7
    Observed Criterion Sigma(I) 2.7
    Resolution(High) 1.98
    Resolution(Low) 122.98
    Number Reflections(All) 70660
    Number Reflections(Observed) 69317
    Percent Possible(Observed) 98.1
     
    High Resolution Shell Details
    Resolution(High) 1.98
    Resolution(Low) 2.08
    Percent Possible(All) 91.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.98
    Resolution(Low) 49.103
    Cut-off Sigma(F) 2.7
    Number of Reflections(all) 67391
    Number of Reflections(Observed) 66548
    Number of Reflections(R-Free) 3559
    Percent Reflections(Observed) 98.75
    R-Factor(Observed) 0.18933
    R-Work 0.18754
    R-Free 0.22191
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 41.854
    Anisotropic B[1][1] -0.49
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.44
    Anisotropic B[2][2] 0.31
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.15
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.98
    Shell Resolution(Low) 2.03
    Number of Reflections(R-Free) 265
    Number of Reflections(R-Work) 4608
    R-Factor(R-Work) 0.293
    R-Factor(R-Free) 0.336
    Percent Reflections(Observed) 92.57
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 5.15
    r_scbond_it 3.47
    r_mcangle_it 2.124
    r_mcbond_it 1.372
    r_gen_planes_refined 0.01
    r_chiral_restr 0.126
    r_dihedral_angle_4_deg 16.296
    r_dihedral_angle_3_deg 15.149
    r_dihedral_angle_2_deg 36.673
    r_dihedral_angle_1_deg 5.475
    r_angle_refined_deg 1.673
    r_bond_refined_d 0.022
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7474
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 489
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution Phenix
    Structure Refinement REFMAC 5.5.0110
     
    Software
    refinement REFMAC version: 5.5.0110
    model building Phenix
    data collection ADSC version: Quantum