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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4I1U
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Temperature 289.0
    Details BuviA.00139.a.B1 PS01581 at 26.1 mg/mL against MCSG 1 screen condition G5, 2 M ammonium sulfate, 0.1 M BisTris pH 6.5, with 20% ethylene glycol as cryo-protectant, crystal tracking ID 236782g5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 116.42 α = 90
    b = 116.42 β = 90
    c = 89.97 γ = 120
     
    Space Group
    Space Group Name:    P 32 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RIGAKU SATURN 944+
    Details VariMax
    Collection Date 2012-08-28
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU FR-E+ SUPERBRIGHT
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.05
    Resolution(Low) 50
    Number Reflections(All) 44492
    Number Reflections(Observed) 44198
    Percent Possible(Observed) 99.3
    R Merge I(Observed) 0.073
    B(Isotropic) From Wilson Plot 34.916
    Redundancy 10.3
     
    High Resolution Shell Details
    Resolution(High) 2.05
    Resolution(Low) 2.1
    Percent Possible(All) 97.6
    R Merge I(Observed) 0.417
    Mean I Over Sigma(Observed) 4.57
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.05
    Resolution(Low) 44.02
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 44196
    Number of Reflections(R-Free) 2234
    Percent Reflections(Observed) 99.33
    R-Factor(Observed) 0.2028
    R-Work 0.2012
    R-Free 0.2338
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 33.514
    Anisotropic B[1][1] 0.22
    Anisotropic B[1][2] 0.22
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.22
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.71
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.05
    Shell Resolution(Low) 2.103
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 3033
    R-Factor(R-Work) 0.227
    R-Factor(R-Free) 0.26
    Percent Reflections(Observed) 97.46
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.007
    r_chiral_restr 0.085
    r_dihedral_angle_4_deg 19.725
    r_dihedral_angle_3_deg 14.206
    r_dihedral_angle_2_deg 35.287
    r_dihedral_angle_1_deg 5.761
    r_angle_other_deg 0.81
    r_angle_refined_deg 1.46
    r_bond_other_d 0.001
    r_bond_refined_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3052
    Nucleic Acid Atoms 0
    Heterogen Atoms 55
    Solvent Atoms 296
     
     
  •   Software and Computing Hide
    Computing
    Data Collection StructureStudio
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    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 Xscale