POP-OUT | CLOSE

An Information Portal to 106082 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1SX4
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.5
    Temperature 298.0
    Details PEG 3000, cacodylic acid, sodium glutamate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 255.26 α = 90
    b = 265.25 β = 90
    c = 184.4 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 3
    Resolution(Low) 40
    Number Reflections(All) 241858
    Number Reflections(Observed) 241858
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.0
    Resolution(Low) 40.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 241858
    Number of Reflections(Observed) 241858
    Number of Reflections(R-Free) 12042
    R-Factor(All) 0.259
    R-Factor(Observed) 0.259
    R-Work 0.2575
    R-Free 0.2873
     
    Temperature Factor Modeling
    Mean Isotropic B Value 2.458
    Anisotropic B[1][1] -3.182
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -2.907
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 6.089
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0
    Shell Resolution(Low) 3.0775
    Number of Reflections(R-Free) 801
    Number of Reflections(R-Work) 15875
    R-Factor(R-Work) 0.347
    R-Factor(R-Free) 0.381
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.077
    Shell Resolution(Low) 3.1613
    Number of Reflections(R-Free) 844
    Number of Reflections(R-Work) 16193
    R-Factor(R-Work) 0.324
    R-Factor(R-Free) 0.354
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.161
    Shell Resolution(Low) 3.2523
    Number of Reflections(R-Free) 894
    Number of Reflections(R-Work) 15772
    R-Factor(R-Work) 0.308
    R-Factor(R-Free) 0.33
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.252
    Shell Resolution(Low) 3.3517
    Number of Reflections(R-Free) 795
    Number of Reflections(R-Work) 15591
    R-Factor(R-Work) 0.301
    R-Factor(R-Free) 0.347
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.352
    Shell Resolution(Low) 3.4609
    Number of Reflections(R-Free) 783
    Number of Reflections(R-Work) 15051
    R-Factor(R-Work) 0.286
    R-Factor(R-Free) 0.331
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.461
    Shell Resolution(Low) 3.5814
    Number of Reflections(R-Free) 736
    Number of Reflections(R-Work) 14685
    R-Factor(R-Work) 0.261
    R-Factor(R-Free) 0.297
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.581
    Shell Resolution(Low) 3.7154
    Number of Reflections(R-Free) 758
    Number of Reflections(R-Work) 14133
    R-Factor(R-Work) 0.255
    R-Factor(R-Free) 0.286
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.715
    Shell Resolution(Low) 3.8657
    Number of Reflections(R-Free) 732
    Number of Reflections(R-Work) 13541
    R-Factor(R-Work) 0.254
    R-Factor(R-Free) 0.273
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.866
    Shell Resolution(Low) 4.0359
    Number of Reflections(R-Free) 680
    Number of Reflections(R-Work) 13104
    R-Factor(R-Work) 0.24
    R-Factor(R-Free) 0.265
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.036
    Shell Resolution(Low) 4.2308
    Number of Reflections(R-Free) 645
    Number of Reflections(R-Work) 12465
    R-Factor(R-Work) 0.226
    R-Factor(R-Free) 0.271
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.231
    Shell Resolution(Low) 4.4568
    Number of Reflections(R-Free) 621
    Number of Reflections(R-Work) 11837
    R-Factor(R-Work) 0.222
    R-Factor(R-Free) 0.263
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.457
    Shell Resolution(Low) 4.7235
    Number of Reflections(R-Free) 600
    Number of Reflections(R-Work) 11249
    R-Factor(R-Work) 0.229
    R-Factor(R-Free) 0.263
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.724
    Shell Resolution(Low) 5.0447
    Number of Reflections(R-Free) 539
    Number of Reflections(R-Work) 10561
    R-Factor(R-Work) 0.24
    R-Factor(R-Free) 0.27
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.045
    Shell Resolution(Low) 5.4416
    Number of Reflections(R-Free) 520
    Number of Reflections(R-Work) 9971
    R-Factor(R-Work) 0.264
    R-Factor(R-Free) 0.276
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.442
    Shell Resolution(Low) 5.95
    Number of Reflections(R-Free) 515
    Number of Reflections(R-Work) 9225
    R-Factor(R-Work) 0.293
    R-Factor(R-Free) 0.329
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.95
    Shell Resolution(Low) 6.634
    Number of Reflections(R-Free) 445
    Number of Reflections(R-Work) 8422
    R-Factor(R-Work) 0.278
    R-Factor(R-Free) 0.313
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.634
    Shell Resolution(Low) 7.6254
    Number of Reflections(R-Free) 380
    Number of Reflections(R-Work) 7511
    R-Factor(R-Work) 0.216
    R-Factor(R-Free) 0.237
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.625
    Shell Resolution(Low) 9.2555
    Number of Reflections(R-Free) 333
    Number of Reflections(R-Work) 6413
    R-Factor(R-Work) 0.187
    R-Factor(R-Free) 0.219
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.255
    Shell Resolution(Low) 12.7523
    Number of Reflections(R-Free) 263
    Number of Reflections(R-Work) 5092
    R-Factor(R-Work) 0.191
    R-Factor(R-Free) 0.206
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 12.752
    Shell Resolution(Low) 40.0
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 3125
    R-Factor(R-Work) 0.388
    R-Factor(R-Free) 0.373
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 1.018
    r_bond_refined_d 0.024
    r_angle_refined_deg 2.034
    r_dihedral_angle_1_deg 6.691
    r_chiral_restr 0.122
    r_gen_planes_refined 0.006
    r_xyhbond_nbd_refined 0.172
    r_metal_ion_refined 0.199
    r_symmetry_vdw_refined 0.315
    r_symmetry_hbond_refined 0.248
    r_mcbond_it 0.236
    r_mcangle_it 0.384
    r_scbond_it 0.702
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 59080
    Nucleic Acid Atoms 0
    Heterogen Atoms 196
    Solvent Atoms 181
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution X-PLOR
    Structure Refinement REFMAC 5
     
    Software
    refinement REFMAC5 (CCP4: Supported Program) version: refmac_5.1.19