POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4JCX
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    Temperature 289.0
    Details Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl, pH 8.2, 1 mM DTT and 1 mM EDTA. Crystallisation conditions: 0.2 M ammonium chloride, 0.1 M MES pH 6.0, 20 % (w/v) PEG6K, protein dimer/DNA molar ratio 1:2, protein concentration 1.2 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 62.2 α = 90
    b = 62.2 β = 90
    c = 147.8 γ = 120
     
    Space Group
    Space Group Name:    P 61
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 120
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2010-11-23
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-4
    Wavelength List 0.93930
    Site ESRF
    Beamline ID14-4
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.3
    Resolution(Low) 50.61
    Number Reflections(All) 14413
    Number Reflections(Observed) 14402
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.111
    B(Isotropic) From Wilson Plot 29.7
    Redundancy 6.0
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.39
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.557
    Mean I Over Sigma(Observed) 3.2
    Redundancy 6.1
    Number Unique Reflections(All) 1642
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.3
    Resolution(Low) 50.61
    Number of Reflections(all) 13586
    Number of Reflections(Observed) 13576
    Number of Reflections(R-Free) 773
    Percent Reflections(Observed) 99.9
    R-Factor(Observed) 0.17309
    R-Work 0.17176
    R-Free 0.19647
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model isotropic
    Mean Isotropic B Value 36.251
    Anisotropic B[1][1] -0.25
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.25
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.5
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.36
    Number of Reflections(Observed) 1020
    Number of Reflections(R-Free) 39
    Number of Reflections(R-Work) 1020
    R-Factor(R-Work) 0.264
    R-Factor(R-Free) 0.299
    Percent Reflections(Observed) 99.62
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_refined 0.005
    r_chiral_restr 0.065
    r_dihedral_angle_4_deg 16.31
    r_dihedral_angle_3_deg 16.47
    r_dihedral_angle_2_deg 37.746
    r_dihedral_angle_1_deg 4.59
    r_angle_refined_deg 1.036
    r_bond_refined_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1541
    Nucleic Acid Atoms 855
    Heterogen Atoms 0
    Solvent Atoms 57
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MXCuBE
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement REFMAC 5.7.0029
     
    Software
    refinement REFMAC version: 5.7.0029
    model building PHASER
    data collection MXCuBE