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X-RAY DIFFRACTION
Materials and Methods page
3DMU
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8
    Temperature 277.0
    Details 44% MPD, 25 mM Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 48.22 α = 90
    b = 48.22 β = 90
    c = 63.28 γ = 90
     
    Space Group
    Space Group Name:    P 41
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type BRUKER APEX II
    Details multi-layer optics
    Collection Date 2005-01-20
     
    Diffraction Radiation
    Monochromator GE111
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SEALED TUBE
    Type OTHER
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.75
    Resolution(Low) 17.98
    Number Reflections(All) 14741
    Number Reflections(Observed) 14710
    Percent Possible(Observed) 99.8
    R Merge I(Observed) 0.0301
    B(Isotropic) From Wilson Plot 33.1
    Redundancy 10.6
     
    High Resolution Shell Details
    Resolution(High) 1.75
    Resolution(Low) 1.84
    Percent Possible(All) 99.3
    R Merge I(Observed) 0.2839
    Mean I Over Sigma(Observed) 4.05
    R-Sym I(Observed) 0.2574
    Redundancy 3.43
    Number Unique Reflections(All) 2016
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 17.0
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 13483
    Number of Reflections(Observed) 12753
    Number of Reflections(R-Free) 1272
    Percent Reflections(Observed) 94.61
    R-Factor(All) 0.23
    R-Factor(Observed) 0.203
    R-Work 0.198
    R-Free 0.255
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 27.909
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.846
    Number of Reflections(Observed) 1091
    Number of Reflections(R-Free) 98
    Number of Reflections(R-Work) 749
    R-Factor(R-Work) 0.251
    R-Factor(R-Free) 0.383
    Percent Reflections(Observed) 85.3
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.846
    Shell Resolution(Low) 1.896
    Number of Reflections(Observed) 1030
    Number of Reflections(R-Free) 66
    R-Factor(R-Work) 0.232
    R-Factor(R-Free) 0.31
    Percent Reflections(Observed) 87.241
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.896
    Shell Resolution(Low) 1.95
    Number of Reflections(Observed) 1027
    Number of Reflections(R-Free) 94
    R-Factor(R-Work) 0.198
    R-Factor(R-Free) 0.255
    Percent Reflections(Observed) 89.496
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.95
    Shell Resolution(Low) 2.01
    Number of Reflections(Observed) 979
    Number of Reflections(R-Free) 83
    R-Factor(R-Work) 0.218
    R-Factor(R-Free) 0.327
    Percent Reflections(Observed) 91.183
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.01
    Shell Resolution(Low) 2.075
    Number of Reflections(Observed) 949
    Number of Reflections(R-Free) 78
    R-Factor(R-Work) 0.215
    R-Factor(R-Free) 0.299
    Percent Reflections(Observed) 93.915
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.075
    Shell Resolution(Low) 2.146
    Number of Reflections(Observed) 934
    Number of Reflections(R-Free) 76
    R-Factor(R-Work) 0.206
    R-Factor(R-Free) 0.284
    Percent Reflections(Observed) 94.639
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 7.239
    r_scbond_it 5.07
    r_mcangle_it 3.159
    r_mcbond_it 2.056
    r_gen_planes_refined 0.005
    r_chiral_restr 0.157
    r_dihedral_angle_4_deg 20.903
    r_dihedral_angle_3_deg 18.093
    r_dihedral_angle_2_deg 29.248
    r_dihedral_angle_1_deg 7.47
    r_angle_refined_deg 2.08
    r_bond_refined_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1007
    Nucleic Acid Atoms 0
    Heterogen Atoms 13
    Solvent Atoms 73
     
     
  •   Software and Computing Hide
    Computing
    Data Collection APEX
    Data Reduction (intensity integration) SAINT
    Data Reduction (data scaling) SAINT
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0017
     
    Software
    data extraction pdb_extract version: 3.005
    refinement REFMAC5 version: 5.5.0017
    density modification DM version: 6.0.99d
    molecular replacement Phaser
    data processing SAINT
    collection/data indexing SAINT