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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3VEK
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 293.0
    Details 20% PEG 6000, 0.01M ZnCl2, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 35.19 α = 72.39
    b = 62.42 β = 74.57
    c = 66.05 γ = 73.63
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector AREA DETECTOR
    Type MAR scanner 345 mm plate
    Collection Date 2011-09-15
     
    Diffraction Radiation
    Monochromator CONFOCAL MAXFLUX MIRRORS
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU MICROMAX-007 HF
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.63
    Resolution(Low) 50
    Number Reflections(All) 14526
    Number Reflections(Observed) 14526
    Percent Possible(Observed) 97.0
    R Merge I(Observed) 0.088
    Redundancy 4.7
     
    High Resolution Shell Details
    Resolution(High) 2.63
    Resolution(Low) 2.68
    Percent Possible(All) 94.3
    R Merge I(Observed) 0.373
    Redundancy 4.4
    Number Unique Reflections(All) 718
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.63
    Resolution(Low) 48.68
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 14469
    Number of Reflections(Observed) 14469
    Number of Reflections(R-Free) 732
    Percent Reflections(Observed) 96.32
    R-Factor(Observed) 0.2369
    R-Work 0.2349
    R-Free 0.2751
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 65.7281
    Anisotropic B[1][1] 0.1
    Anisotropic B[1][2] -1.22
    Anisotropic B[1][3] 0.59
    Anisotropic B[2][2] 4.33
    Anisotropic B[2][3] 1.29
    Anisotropic B[3][3] -4.85
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.628
    Shell Resolution(Low) 2.696
    Number of Reflections(R-Free) 56
    Number of Reflections(R-Work) 963
    R-Factor(R-Work) 0.404
    R-Factor(R-Free) 0.455
    Percent Reflections(Observed) 91.23
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.988
    r_scbond_it 1.25
    r_mcangle_it 0.977
    r_mcbond_other 0.081
    r_bond_refined_d 0.004
    r_bond_other_d 0.001
    r_angle_refined_deg 0.921
    r_angle_other_deg 0.881
    r_dihedral_angle_1_deg 3.746
    r_dihedral_angle_2_deg 25.746
    r_dihedral_angle_3_deg 9.963
    r_dihedral_angle_4_deg 7.481
    r_chiral_restr 0.04
    r_gen_planes_refined 0.002
    r_gen_planes_other 0.001
    r_mcbond_it 0.51
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1512
    Nucleic Acid Atoms 1628
    Heterogen Atoms 14
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0109
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    molecular replacement Phaser version: 2.1.4
    data reduction SCALEPACK
    data collection DENZO