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X-RAY DIFFRACTION
Materials and Methods page
3V9X
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 298.0
    Details 20%(v/v) 2-Propanol, 0.1M MES monohydrate, 20%(w/v) Polyethylene glycol monomethyl ester 2000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 46.28 α = 90
    b = 46.28 β = 90
    c = 314.38 γ = 120
     
    Space Group
    Space Group Name:    P 32
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2010-04-30
     
    Diffraction Radiation
    Monochromator SAGITALLY FOCUSED Si(III)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSRRC BEAMLINE BL13B1
    Wavelength List 0.9999
    Site NSRRC
    Beamline BL13B1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.9
    Resolution(Low) 30
    Number Reflections(All) 58869
    Number Reflections(Observed) 58869
    Percent Possible(Observed) 98.9
    Redundancy 3.0
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 1.97
    Percent Possible(All) 99.9
    Mean I Over Sigma(Observed) 3.98
    R-Sym I(Observed) 0.353
    Redundancy 3.1
    Number Unique Reflections(All) 5942
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.9
    Resolution(Low) 23.27
    Cut-off Sigma(F) 1.97
    Number of Reflections(all) 58768
    Number of Reflections(Observed) 58768
    Number of Reflections(R-Free) 4567
    Percent Reflections(Observed) 98.9
    R-Factor(Observed) 0.1877
    R-Work 0.1847
    R-Free 0.2228
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 27.8563
    Anisotropic B[1][1] 2.5911
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.5911
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -5.1821
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8997
    Shell Resolution(Low) 1.9213
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1923
    R-Factor(R-Work) 0.2564
    R-Factor(R-Free) 0.3614
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9213
    Shell Resolution(Low) 1.9439
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 1806
    R-Factor(R-Work) 0.2298
    R-Factor(R-Free) 0.2873
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9439
    Shell Resolution(Low) 1.9676
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 1758
    R-Factor(R-Work) 0.2221
    R-Factor(R-Free) 0.2854
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9676
    Shell Resolution(Low) 1.9925
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 1873
    R-Factor(R-Work) 0.2189
    R-Factor(R-Free) 0.256
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9925
    Shell Resolution(Low) 2.0187
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1842
    R-Factor(R-Work) 0.2168
    R-Factor(R-Free) 0.2888
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0187
    Shell Resolution(Low) 2.0463
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 1780
    R-Factor(R-Work) 0.2082
    R-Factor(R-Free) 0.2623
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0463
    Shell Resolution(Low) 2.0755
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 1824
    R-Factor(R-Work) 0.1946
    R-Factor(R-Free) 0.2456
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0755
    Shell Resolution(Low) 2.1065
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 1890
    R-Factor(R-Work) 0.2044
    R-Factor(R-Free) 0.2575
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1065
    Shell Resolution(Low) 2.1394
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 1731
    R-Factor(R-Work) 0.1875
    R-Factor(R-Free) 0.2591
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1394
    Shell Resolution(Low) 2.1745
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 1824
    R-Factor(R-Work) 0.2067
    R-Factor(R-Free) 0.2855
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1745
    Shell Resolution(Low) 2.2119
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 1846
    R-Factor(R-Work) 0.2052
    R-Factor(R-Free) 0.2593
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2119
    Shell Resolution(Low) 2.2521
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 1764
    R-Factor(R-Work) 0.1898
    R-Factor(R-Free) 0.2767
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2521
    Shell Resolution(Low) 2.2954
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1896
    R-Factor(R-Work) 0.1967
    R-Factor(R-Free) 0.2681
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2954
    Shell Resolution(Low) 2.3422
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1802
    R-Factor(R-Work) 0.1975
    R-Factor(R-Free) 0.2826
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3422
    Shell Resolution(Low) 2.3931
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 1782
    R-Factor(R-Work) 0.1879
    R-Factor(R-Free) 0.2454
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3931
    Shell Resolution(Low) 2.4487
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1908
    R-Factor(R-Work) 0.1955
    R-Factor(R-Free) 0.2229
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4487
    Shell Resolution(Low) 2.5099
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1761
    R-Factor(R-Work) 0.1876
    R-Factor(R-Free) 0.2499
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5099
    Shell Resolution(Low) 2.5776
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 1892
    R-Factor(R-Work) 0.1955
    R-Factor(R-Free) 0.2866
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5776
    Shell Resolution(Low) 2.6534
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1792
    R-Factor(R-Work) 0.2022
    R-Factor(R-Free) 0.2449
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6534
    Shell Resolution(Low) 2.7389
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 1811
    R-Factor(R-Work) 0.1951
    R-Factor(R-Free) 0.2509
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7389
    Shell Resolution(Low) 2.8366
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 1768
    R-Factor(R-Work) 0.1845
    R-Factor(R-Free) 0.2289
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8366
    Shell Resolution(Low) 2.95
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1818
    R-Factor(R-Work) 0.1859
    R-Factor(R-Free) 0.21
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.95
    Shell Resolution(Low) 3.084
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 1863
    R-Factor(R-Work) 0.1866
    R-Factor(R-Free) 0.2437
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.084
    Shell Resolution(Low) 3.2461
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1733
    R-Factor(R-Work) 0.1803
    R-Factor(R-Free) 0.2033
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2461
    Shell Resolution(Low) 3.4489
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 1710
    R-Factor(R-Work) 0.1722
    R-Factor(R-Free) 0.1955
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4489
    Shell Resolution(Low) 3.7142
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1761
    R-Factor(R-Work) 0.16
    R-Factor(R-Free) 0.1928
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7142
    Shell Resolution(Low) 4.0862
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1694
    R-Factor(R-Work) 0.1538
    R-Factor(R-Free) 0.1699
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0862
    Shell Resolution(Low) 4.6733
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 1772
    R-Factor(R-Work) 0.1491
    R-Factor(R-Free) 0.1755
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6733
    Shell Resolution(Low) 5.8722
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 1811
    R-Factor(R-Work) 0.1777
    R-Factor(R-Free) 0.171
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8722
    Shell Resolution(Low) 23.2715
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1766
    R-Factor(R-Work) 0.1945
    R-Factor(R-Free) 0.1849
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.563
    f_plane_restr 0.004
    f_chiral_restr 0.065
    f_angle_d 0.93
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6387
    Nucleic Acid Atoms 272
    Heterogen Atoms 8
    Solvent Atoms 524
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution AMoRE
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building AMoRE
    data collection HKL-2000