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X-RAY DIFFRACTION
Materials and Methods page
3W1I
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 293.0
    Details 120mM Tris-HCl, 11% PEG 4000, 400mM CaCl2, 160mM KCl, 5.0mM NiCl2, 50mM Na2S2O3, 50mM L-serine, 0.2M NaCl, 10mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 92.82 α = 90
    b = 280.94 β = 113.45
    c = 97.64 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 90
    Diffrn ID 2
    Data Collection Temperature 90
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Details mirrors
    Collection Date 2008-02-19
    Detector CCD
    Type ADSC QUANTUM 270
    Details mirrors
    Collection Date 2008-03-04
     
    Diffraction Radiation
    Monochromator Si
    Diffraction Protocol MAD
    Monochromator Si
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL41XU
    Wavelength List 0.97917, 0.97947
    Site SPRING-8
    Beamline BL41XU
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE BL-17A
    Wavelength List 1.07117
    Site PHOTON FACTORY
    Beamline BL-17A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -2.0
    Resolution(High) 3.19
    Resolution(Low) 50
    Number Reflections(All) 75523
    Number Reflections(Observed) 75145
    Percent Possible(Observed) 99.5
    R Merge I(Observed) 0.09
    Redundancy 7.4
     
    High Resolution Shell Details
    Resolution(High) 3.2
    Resolution(Low) 3.31
    Percent Possible(All) 96.0
    R Merge I(Observed) 0.674
    Mean I Over Sigma(Observed) 2.5
    R-Sym I(Observed) 0.674
    Redundancy 6.2
    Number Unique Reflections(All) 7513
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MAD
    reflnsShellList 3.192
    Resolution(Low) 48.941
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 75789
    Number of Reflections(Observed) 75046
    Number of Reflections(R-Free) 3750
    Percent Reflections(Observed) 99.02
    R-Factor(Observed) 0.1769
    R-Work 0.1738
    R-Free 0.2354
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 130.118
    Anisotropic B[1][1] -21.7714
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -6.6801
    Anisotropic B[2][2] -9.6703
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 31.4417
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1925
    Shell Resolution(Low) 3.2329
    Number of Reflections(R-Free) 105
    Number of Reflections(R-Work) 2173
    R-Factor(R-Work) 0.2771
    R-Factor(R-Free) 0.3679
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2329
    Shell Resolution(Low) 3.2754
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2554
    R-Factor(R-Work) 0.272
    R-Factor(R-Free) 0.3376
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2754
    Shell Resolution(Low) 3.3202
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2623
    R-Factor(R-Work) 0.2803
    R-Factor(R-Free) 0.3303
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3202
    Shell Resolution(Low) 3.3677
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2707
    R-Factor(R-Work) 0.2634
    R-Factor(R-Free) 0.3644
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3677
    Shell Resolution(Low) 3.4179
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2567
    R-Factor(R-Work) 0.2588
    R-Factor(R-Free) 0.3128
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4179
    Shell Resolution(Low) 3.4713
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2726
    R-Factor(R-Work) 0.2327
    R-Factor(R-Free) 0.2863
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4713
    Shell Resolution(Low) 3.5282
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2620
    R-Factor(R-Work) 0.231
    R-Factor(R-Free) 0.3236
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5282
    Shell Resolution(Low) 3.589
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2689
    R-Factor(R-Work) 0.23
    R-Factor(R-Free) 0.3083
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.589
    Shell Resolution(Low) 3.6543
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2621
    R-Factor(R-Work) 0.2164
    R-Factor(R-Free) 0.2576
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6543
    Shell Resolution(Low) 3.7245
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2709
    R-Factor(R-Work) 0.2163
    R-Factor(R-Free) 0.3154
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7245
    Shell Resolution(Low) 3.8005
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.2027
    R-Factor(R-Free) 0.305
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8005
    Shell Resolution(Low) 3.8831
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 2667
    R-Factor(R-Work) 0.1874
    R-Factor(R-Free) 0.2548
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8831
    Shell Resolution(Low) 3.9734
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2622
    R-Factor(R-Work) 0.1783
    R-Factor(R-Free) 0.2307
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9734
    Shell Resolution(Low) 4.0728
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2726
    R-Factor(R-Work) 0.1693
    R-Factor(R-Free) 0.2456
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0728
    Shell Resolution(Low) 4.1828
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2632
    R-Factor(R-Work) 0.1687
    R-Factor(R-Free) 0.2374
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1828
    Shell Resolution(Low) 4.3058
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2623
    R-Factor(R-Work) 0.1648
    R-Factor(R-Free) 0.2453
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3058
    Shell Resolution(Low) 4.4447
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.1388
    R-Factor(R-Free) 0.1876
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4447
    Shell Resolution(Low) 4.6035
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2641
    R-Factor(R-Work) 0.1287
    R-Factor(R-Free) 0.1847
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6035
    Shell Resolution(Low) 4.7876
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2671
    R-Factor(R-Work) 0.1195
    R-Factor(R-Free) 0.1764
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7876
    Shell Resolution(Low) 5.0053
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2686
    R-Factor(R-Work) 0.1354
    R-Factor(R-Free) 0.1974
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0053
    Shell Resolution(Low) 5.2689
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2669
    R-Factor(R-Work) 0.1492
    R-Factor(R-Free) 0.2267
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2689
    Shell Resolution(Low) 5.5986
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2680
    R-Factor(R-Work) 0.1665
    R-Factor(R-Free) 0.2385
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5986
    Shell Resolution(Low) 6.0302
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.2011
    R-Factor(R-Free) 0.2406
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0302
    Shell Resolution(Low) 6.6357
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2693
    R-Factor(R-Work) 0.2014
    R-Factor(R-Free) 0.2917
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6357
    Shell Resolution(Low) 7.5928
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2664
    R-Factor(R-Work) 0.1666
    R-Factor(R-Free) 0.2291
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.5928
    Shell Resolution(Low) 9.5544
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2678
    R-Factor(R-Work) 0.1263
    R-Factor(R-Free) 0.1781
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.5544
    Shell Resolution(Low) 48.947
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2646
    R-Factor(R-Work) 0.1756
    R-Factor(R-Free) 0.2104
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.459
    f_plane_restr 0.004
    f_chiral_restr 0.071
    f_angle_d 1.22
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 30712
    Nucleic Acid Atoms 0
    Heterogen Atoms 7
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution autoSHARP
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    density modification DM
    data reduction HKL