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X-RAY DIFFRACTION
Materials and Methods page
4M6D
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7
    Temperature 298.0
    Details 1.1M Malonic Acid, 0.15 M Ammonium Citrate Tribasic, 0.072 M Succinic Acid, 0.18 M DL-Malic Acid, 0.24 M Sodium Acetate, 0.3 M Sodium Formate, 0.096 M Ammonium Tartrate Dibasic, Final pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 43.91 α = 118.59
    b = 132.29 β = 96.39
    c = 131.54 γ = 96.27
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2013-01-18
     
    Diffraction Radiation
    Diffraction Protocol SAD
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.075
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.68
    Resolution(Low) 50
    Number Reflections(Observed) 67209
    Percent Possible(Observed) 94.9
    R Merge I(Observed) 0.067
    Redundancy 1.9
     
    High Resolution Shell Details
    Resolution(High) 2.7
    Resolution(Low) 2.75
    Percent Possible(All) 90.9
    R Merge I(Observed) 0.629
    Redundancy 1.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.68
    Resolution(Low) 38.04
    Number of Reflections(Observed) 53394
    Number of Reflections(R-Free) 3007
    Percent Reflections(Observed) 79.53
    R-Factor(Observed) 0.16832
    R-Work 0.16549
    R-Free 0.216
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 122.84
    Anisotropic B[1][1] -33.08
    Anisotropic B[1][2] -1.5
    Anisotropic B[1][3] -4.37
    Anisotropic B[2][2] 74.15
    Anisotropic B[2][3] -12.52
    Anisotropic B[3][3] -41.07
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.685
    Shell Resolution(Low) 2.754
    Number of Reflections(R-Free) 13
    Number of Reflections(R-Work) 338
    R-Factor(R-Work) 0.196
    R-Factor(R-Free) 0.277
    Percent Reflections(Observed) 6.64
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 53.84
    r_rigid_bond_restr 8.222
    r_scbond_it 1.995
    r_mcangle_it 3.878
    r_mcbond_it 2.263
    r_gen_planes_refined 0.006
    r_chiral_restr 0.094
    r_dihedral_angle_4_deg 18.677
    r_dihedral_angle_3_deg 18.936
    r_dihedral_angle_2_deg 38.809
    r_dihedral_angle_1_deg 7.51
    r_angle_refined_deg 1.421
    r_bond_refined_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6006
    Nucleic Acid Atoms 5357
    Heterogen Atoms 0
    Solvent Atoms 69
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement REFMAC 5.7.0029
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    molecular replacement Phaser version: 2.5.1
    data reduction SCALEPACK