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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4LDW
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Temperature 293.0
    Details 1 4 mg/mL ARF1DBD + 1 l crystallization buffer (100 mM MES 6.5, 20%PEG 5K MME) 7.7.11), VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 73.26 α = 90
    b = 83.67 β = 117.61
    c = 79.03 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2011-07-15
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-4
    Wavelength List 0.9393
    Site ESRF
    Beamline ID14-4
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.67
    Resolution(Low) 70.02
    Number Reflections(Observed) 23332
    Percent Possible(Observed) 96.6
    R Merge I(Observed) 0.098
    B(Isotropic) From Wilson Plot 73.1
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 2.67
    Resolution(Low) 2.81
    Percent Possible(All) 96.2
    R Merge I(Observed) 0.65
    Mean I Over Sigma(Observed) 2.2
    Redundancy 3.7
    Number Unique Reflections(All) 3391
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.67
    Resolution(Low) 35.94
    Number of Reflections(Observed) 22140
    Number of Reflections(R-Free) 1173
    Percent Reflections(Observed) 96.1
    R-Factor(Observed) 0.21885
    R-Work 0.21561
    R-Free 0.27945
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 69.443
    Anisotropic B[1][1] -0.52
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.32
    Anisotropic B[2][2] -2.85
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.73
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.667
    Shell Resolution(Low) 2.736
    Number of Reflections(R-Free) 86
    Number of Reflections(R-Work) 1598
    R-Factor(R-Work) 0.32
    R-Factor(R-Free) 0.407
    Percent Reflections(Observed) 94.61
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_long_range_B_other 5.464
    r_long_range_B_refined 5.466
    r_scangle_other 3.089
    r_scbond_other 1.869
    r_scbond_it 1.87
    r_mcangle_other 2.939
    r_mcangle_it 2.939
    r_mcbond_other 1.755
    r_mcbond_it 1.756
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.007
    r_chiral_restr 0.081
    r_dihedral_angle_4_deg 19.709
    r_dihedral_angle_3_deg 18.589
    r_dihedral_angle_2_deg 34.693
    r_dihedral_angle_1_deg 6.868
    r_angle_other_deg 0.772
    r_angle_refined_deg 1.481
    r_bond_other_d 0.001
    r_bond_refined_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5104
    Nucleic Acid Atoms 0
    Heterogen Atoms 2
    Solvent Atoms 54
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MXCube
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution phaser
    Structure Refinement REFMAC 5.7.0032
     
    Software
    refinement REFMAC version: 5.7.0032
    model building phaser
    data collection MXCube