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X-RAY DIFFRACTION
Materials and Methods page
4DGG
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, sitting drop
    pH 6.5
    Temperature 298.0
    Details 6% PEG 20000, 100 mM MES pH 6.5, 2.0 mM RM-1-176 in 10% DMSO, vapor diffusion, sitting drop, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 42.17 α = 78.73
    b = 63.48 β = 88.48
    c = 74 γ = 89.93
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type PSI PILATUS 6M
    Collection Date 2010-12-09
     
    Diffraction Radiation
    Monochromator Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs.
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL12-2
    Wavelength List 0.9795
    Site SSRL
    Beamline BL12-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.65
    Resolution(Low) 52.6
    Number Reflections(All) 17677
    Number Reflections(Observed) 17677
    Percent Possible(Observed) 81.0
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 2.65
    Resolution(Low) 2.79
    Percent Possible(All) 72.9
    R Merge I(Observed) 0.01
    Mean I Over Sigma(Observed) 0.7
    R-Sym I(Observed) 1.011
    Redundancy 3.7
    Number Unique Reflections(All) 2313
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.65
    Resolution(Low) 72.55
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 17677
    Number of Reflections(R-Free) 866
    Percent Reflections(Observed) 80.85
    R-Factor(Observed) 0.2102
    R-Work 0.2081
    R-Free 0.2518
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 39.6264
    Anisotropic B[1][1] 0.05
    Anisotropic B[1][2] 0.56
    Anisotropic B[1][3] -0.8
    Anisotropic B[2][2] -1.17
    Anisotropic B[2][3] 1.11
    Anisotropic B[3][3] 0.73
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.65
    Shell Resolution(Low) 2.719
    Number of Reflections(R-Free) 75
    Number of Reflections(R-Work) 1172
    R-Factor(R-Work) 0.38
    R-Factor(R-Free) 0.376
    Percent Reflections(Observed) 78.23
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.003
    r_gen_planes_refined 0.005
    r_chiral_restr 0.066
    r_dihedral_angle_4_deg 14.461
    r_dihedral_angle_3_deg 15.207
    r_dihedral_angle_2_deg 36.648
    r_dihedral_angle_1_deg 5.96
    r_angle_other_deg 0.983
    r_angle_refined_deg 1.304
    r_bond_other_d 0.003
    r_bond_refined_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4173
    Nucleic Acid Atoms 0
    Heterogen Atoms 64
    Solvent Atoms 13
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BLU-ICE
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Refinement REFMAC 5.6.0117
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5
    data reduction SCALA version: 3.3.20