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X-RAY DIFFRACTION
Materials and Methods page
3D4D
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 8
    Temperature 277.0
    Details 25% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 8.0, vapor diffusion, hanging drop, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 31.02 α = 90
    b = 81.29 β = 90.05
    c = 60.38 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 110
     
    Diffraction Detector
    Detector CCD
    Type BRUKER APEX II
    Details multi-layer optics
    Collection Date 2008-02-06
     
    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) 2
    Resolution(Low) 60.38
    Number Reflections(All) 17596
    Number Reflections(Observed) 17583
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.0635
    B(Isotropic) From Wilson Plot 20.5
    Redundancy 11.3
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.1
    Percent Possible(All) 2296.0
    R Merge I(Observed) 0.0996
    Mean I Over Sigma(Observed) 15.41
    R-Sym I(Observed) 0.0594
    Redundancy 4.85
    Number Unique Reflections(All) 2296
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.1
    Resolution(Low) 60.38
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 17570
    Number of Reflections(Observed) 17554
    Number of Reflections(R-Free) 1781
    Percent Reflections(Observed) 99.91
    R-Factor(All) 0.2423
    R-Factor(Observed) 0.239
    R-Work 0.233
    R-Free 0.29
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 8.908
    Anisotropic B[1][1] -0.01
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.01
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.01
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1
    Shell Resolution(Low) 2.155
    Number of Reflections(Observed) 1316
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 1195
    R-Factor(R-Work) 0.205
    R-Factor(R-Free) 0.326
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.155
    Shell Resolution(Low) 2.214
    Number of Reflections(Observed) 1277
    Number of Reflections(R-Free) 134
    R-Factor(R-Work) 0.195
    R-Factor(R-Free) 0.247
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.214
    Shell Resolution(Low) 2.278
    Number of Reflections(Observed) 1204
    Number of Reflections(R-Free) 119
    R-Factor(R-Work) 0.212
    R-Factor(R-Free) 0.34
    Percent Reflections(Observed) 99.917
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.278
    Shell Resolution(Low) 2.348
    Number of Reflections(Observed) 1188
    Number of Reflections(R-Free) 106
    R-Factor(R-Work) 0.219
    R-Factor(R-Free) 0.308
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.348
    Shell Resolution(Low) 2.425
    Number of Reflections(Observed) 1160
    Number of Reflections(R-Free) 107
    R-Factor(R-Work) 0.235
    R-Factor(R-Free) 0.287
    Percent Reflections(Observed) 99.914
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.425
    Shell Resolution(Low) 2.51
    Number of Reflections(Observed) 1106
    Number of Reflections(R-Free) 101
    R-Factor(R-Work) 0.242
    R-Factor(R-Free) 0.285
    Percent Reflections(Observed) 99.91
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.837
    r_scbond_it 1.198
    r_mcangle_it 0.788
    r_mcbond_it 0.545
    r_symmetry_hbond_refined 0.147
    r_symmetry_vdw_refined 0.19
    r_bond_refined_d 0.009
    r_angle_refined_deg 1.316
    r_dihedral_angle_1_deg 6.15
    r_dihedral_angle_2_deg 34.225
    r_dihedral_angle_3_deg 16.847
    r_dihedral_angle_4_deg 11.916
    r_chiral_restr 0.083
    r_gen_planes_refined 0.004
    r_nbd_refined 0.202
    r_nbtor_refined 0.298
    r_xyhbond_nbd_refined 0.147
    r_metal_ion_refined 0.044
     
    Coordinate Error
    Luzzati ESD(Observed) 0.292
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2060
    Nucleic Acid Atoms 0
    Heterogen Atoms 52
    Solvent Atoms 183
     
     
  •   Software and Computing Hide
    Computing
    Data Collection APEX
    Data Reduction (intensity integration) SAINT
    Data Reduction (data scaling) SAINT
    Structure Solution PHASER
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 3.005
    refinement REFMAC5
    molecular replacement Phaser
    collection/data indexing SAINT version: V7.51A