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X-RAY DIFFRACTION
Materials and Methods page
4LDY
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7
    Temperature 293.0
    Details 0.75 l of 13 mg/ml Arf1dbd-g245a +0.75 l crystallization buffer (100 mM bis-tris-propane pH 7.0, 0.7 M succinic acid), VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 73.1 α = 90
    b = 84.24 β = 114.76
    c = 78.96 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 PSI PILATUS 6M
    Collection Date 2012-11-01
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALBA BEAMLINE XALOC
    Wavelength List 0.9795
    Site ALBA
    Beamline XALOC
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.3
    Resolution(Low) 71.7
    Number Reflections(Observed) 38764
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.102
    B(Isotropic) From Wilson Plot 41.1
    Redundancy 3.1
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.42
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.63
    Mean I Over Sigma(Observed) 1.8
    Redundancy 3.2
    Number Unique Reflections(All) 5641
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.3
    Resolution(Low) 63.91
    Number of Reflections(Observed) 36804
    Number of Reflections(R-Free) 1943
    Percent Reflections(Observed) 99.87
    R-Factor(Observed) 0.21263
    R-Work 0.21015
    R-Free 0.2588
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 60.556
    Anisotropic B[1][1] -0.83
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.33
    Anisotropic B[2][2] -0.58
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.56
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.36
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2750
    R-Factor(R-Work) 0.308
    R-Factor(R-Free) 0.326
    Percent Reflections(Observed) 99.97
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_long_range_B_other 7.104
    r_long_range_B_refined 7.115
    r_scangle_other 4.215
    r_scbond_other 2.604
    r_scbond_it 2.604
    r_mcangle_other 3.83
    r_mcangle_it 3.83
    r_mcbond_other 2.368
    r_mcbond_it 2.368
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.008
    r_chiral_restr 0.09
    r_dihedral_angle_4_deg 17.695
    r_dihedral_angle_3_deg 17.289
    r_dihedral_angle_2_deg 35.148
    r_dihedral_angle_1_deg 7.532
    r_angle_other_deg 0.799
    r_angle_refined_deg 1.641
    r_bond_other_d 0.001
    r_bond_refined_d 0.015
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5239
    Nucleic Acid Atoms 0
    Heterogen Atoms 2
    Solvent Atoms 109
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Refinement REFMAC 5.7.0032
     
    Software
    refinement REFMAC version: 5.7.0032