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X-RAY DIFFRACTION
Materials and Methods page
4DG5
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.8
    Temperature 298.0
    Details 0.15M Calcium chloride dihydrate, 0.1M HEPES-Na, 20% (w/v)Polyethylene glycol 2000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 45.14 α = 90
    b = 74.75 β = 95.72
    c = 58.67 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 IMAGE PLATE
    Type RIGAKU RAXIS IV++
    Details Varimax mirror
    Collection Date 2010-12-08
     
    Diffraction Radiation
    Monochromator Varimax optics
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU MICROMAX-007 HF
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 2.0
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 2.3
    Resolution(Low) 58.37
    Number Reflections(All) 16871
    Number Reflections(Observed) 16871
    Percent Possible(Observed) 97.6
    Redundancy 3.7
     
    High Resolution Shell Details
    Resolution(High) 2.3
    Resolution(Low) 2.42
    Percent Possible(All) 95.9
    R Merge I(Observed) 0.235
    Mean I Over Sigma(Observed) 3.2
    R-Sym I(Observed) 0.235
    Redundancy 3.6
    Number Unique Reflections(All) 2401
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.3
    Resolution(Low) 58.37
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 16852
    Number of Reflections(R-Free) 850
    Percent Reflections(Observed) 97.21
    R-Factor(Observed) 0.1769
    R-Work 0.1724
    R-Free 0.2636
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 15.703
    Anisotropic B[1][1] -0.89
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.42
    Anisotropic B[2][2] 0.6
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.21
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3
    Shell Resolution(Low) 2.36
    Number of Reflections(R-Free) 52
    Number of Reflections(R-Work) 1149
    R-Factor(R-Work) 0.169
    R-Factor(R-Free) 0.248
    Percent Reflections(Observed) 94.72
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.179
    r_scbond_it 2.515
    r_mcangle_it 1.416
    r_mcbond_it 0.759
    r_gen_planes_refined 0.007
    r_chiral_restr 0.113
    r_dihedral_angle_4_deg 8.866
    r_dihedral_angle_3_deg 18.141
    r_dihedral_angle_2_deg 40.588
    r_dihedral_angle_1_deg 6.14
    r_angle_refined_deg 1.667
    r_bond_refined_d 0.017
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2985
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 260
     
     
  •   Software and Computing Hide
    Computing
    Data Collection StructureStudio
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.5.0109
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5 version: 5.5.0109
    molecular replacement MOLREP
    data reduction SCALA version: 3.3.9