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X-RAY DIFFRACTION
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1SX3
Re-refined structure
Text THIS ENTRY 1SX3 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R1KP8SF DETERMINED BY THE AUTHOR OF THE PDB ENTRY 1KP8: J.WANG
 
re-refined PDB record
DB record 1KP8
Detail THIS ENTRY 1SX3 REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R1KP8SF
 
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 298.0
    Details PEG 8000, bis-tris propane, ethylene glycol, glycerol, potassium chloride, calcium chloride, ATPgammaS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 135.57 α = 90
    b = 260.11 β = 101.14
    c = 150.2 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 39.841
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 540790
    Number of Reflections(Observed) 540790
    Number of Reflections(R-Free) 10647
    R-Factor(All) 0.246
    R-Factor(Observed) 0.246
    R-Work 0.2455
    R-Free 0.2647
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 13.974
    Anisotropic B[1][1] -3.059
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.01
    Anisotropic B[2][2] -0.144
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 3.206
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.0519
    Number of Reflections(R-Free) 497
    Number of Reflections(R-Work) 24808
    R-Factor(R-Work) 0.473
    R-Factor(R-Free) 0.464
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.052
    Shell Resolution(Low) 2.108
    Number of Reflections(R-Free) 534
    Number of Reflections(R-Work) 26914
    R-Factor(R-Work) 0.444
    R-Factor(R-Free) 0.438
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.108
    Shell Resolution(Low) 2.1689
    Number of Reflections(R-Free) 615
    Number of Reflections(R-Work) 28836
    R-Factor(R-Work) 0.395
    R-Factor(R-Free) 0.397
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.169
    Shell Resolution(Low) 2.2355
    Number of Reflections(R-Free) 575
    Number of Reflections(R-Work) 30010
    R-Factor(R-Work) 0.357
    R-Factor(R-Free) 0.363
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.235
    Shell Resolution(Low) 2.3085
    Number of Reflections(R-Free) 639
    Number of Reflections(R-Work) 31203
    R-Factor(R-Work) 0.329
    R-Factor(R-Free) 0.348
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.309
    Shell Resolution(Low) 2.3893
    Number of Reflections(R-Free) 614
    Number of Reflections(R-Work) 31929
    R-Factor(R-Work) 0.306
    R-Factor(R-Free) 0.311
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.389
    Shell Resolution(Low) 2.4791
    Number of Reflections(R-Free) 656
    Number of Reflections(R-Work) 31948
    R-Factor(R-Work) 0.299
    R-Factor(R-Free) 0.343
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.479
    Shell Resolution(Low) 2.58
    Number of Reflections(R-Free) 617
    Number of Reflections(R-Work) 32157
    R-Factor(R-Work) 0.282
    R-Factor(R-Free) 0.325
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.58
    Shell Resolution(Low) 2.6942
    Number of Reflections(R-Free) 645
    Number of Reflections(R-Work) 31955
    R-Factor(R-Work) 0.263
    R-Factor(R-Free) 0.294
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.694
    Shell Resolution(Low) 2.825
    Number of Reflections(R-Free) 621
    Number of Reflections(R-Work) 31743
    R-Factor(R-Work) 0.246
    R-Factor(R-Free) 0.266
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.825
    Shell Resolution(Low) 2.977
    Number of Reflections(R-Free) 589
    Number of Reflections(R-Work) 31214
    R-Factor(R-Work) 0.231
    R-Factor(R-Free) 0.249
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.977
    Shell Resolution(Low) 3.1565
    Number of Reflections(R-Free) 623
    Number of Reflections(R-Work) 30548
    R-Factor(R-Work) 0.227
    R-Factor(R-Free) 0.267
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.156
    Shell Resolution(Low) 3.3729
    Number of Reflections(R-Free) 591
    Number of Reflections(R-Work) 29503
    R-Factor(R-Work) 0.215
    R-Factor(R-Free) 0.24
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.373
    Shell Resolution(Low) 3.641
    Number of Reflections(R-Free) 602
    Number of Reflections(R-Work) 28032
    R-Factor(R-Work) 0.217
    R-Factor(R-Free) 0.243
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.641
    Shell Resolution(Low) 3.9852
    Number of Reflections(R-Free) 565
    Number of Reflections(R-Work) 25970
    R-Factor(R-Work) 0.211
    R-Factor(R-Free) 0.225
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.985
    Shell Resolution(Low) 4.45
    Number of Reflections(R-Free) 478
    Number of Reflections(R-Work) 23606
    R-Factor(R-Work) 0.198
    R-Factor(R-Free) 0.22
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.45
    Shell Resolution(Low) 5.1277
    Number of Reflections(R-Free) 402
    Number of Reflections(R-Work) 20926
    R-Factor(R-Work) 0.211
    R-Factor(R-Free) 0.234
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.128
    Shell Resolution(Low) 6.2543
    Number of Reflections(R-Free) 358
    Number of Reflections(R-Work) 17711
    R-Factor(R-Work) 0.25
    R-Factor(R-Free) 0.268
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.254
    Shell Resolution(Low) 8.738
    Number of Reflections(R-Free) 284
    Number of Reflections(R-Work) 13558
    R-Factor(R-Work) 0.213
    R-Factor(R-Free) 0.226
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.738
    Shell Resolution(Low) 39.841
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 7572
    R-Factor(R-Work) 0.216
    R-Factor(R-Free) 0.215
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 2.554
    r_scbond_it 1.893
    r_bond_refined_d 0.026
    r_angle_refined_deg 1.961
    r_dihedral_angle_1_deg 5.388
    r_chiral_restr 0.147
    r_gen_planes_refined 0.008
    r_xyhbond_nbd_refined 0.159
    r_metal_ion_refined 0.357
    r_symmetry_vdw_refined 0.428
    r_symmetry_hbond_refined 0.417
    r_symmetry_metal_ion_refined 0.102
    r_mcbond_it 0.624
    r_mcangle_it 0.914
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 53970
    Nucleic Acid Atoms 0
    Heterogen Atoms 464
    Solvent Atoms 946
     
     
  •   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 REFMAC 5 (CCP4: Supported Program) version: refmac_5.1.19