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An Information Portal to 107049 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4KB0
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 293.0
    Details 6% v/v Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25% w/v Polyethylene glycol 4000 , VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 60.26 α = 90
    b = 81.94 β = 105.46
    c = 73.44 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX225HE
    Collection Date 2011-06-03
     
    Diffraction Radiation
    Monochromator SAGITALLY FOCUSED Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL44XU
    Wavelength List 0.9
    Site SPRING-8
    Beamline BL44XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2
    Resolution(Low) 30
    Number Reflections(All) 44590
    Number Reflections(Observed) 44590
    Percent Possible(Observed) 96.4
    Redundancy 4.0
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.07
    Percent Possible(All) 91.0
    Mean I Over Sigma(Observed) 2.36
    R-Sym I(Observed) 0.468
    Redundancy 3.2
    Number Unique Reflections(All) 4176
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.004
    Resolution(Low) 29.799
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 44562
    Number of Reflections(Observed) 44562
    Number of Reflections(R-Free) 3468
    Percent Reflections(Observed) 96.25
    R-Factor(All) 0.1902
    R-Factor(Observed) 0.1902
    R-Work 0.1885
    R-Free 0.2106
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0037
    Shell Resolution(Low) 2.0311
    Number of Reflections(R-Free) 108
    Number of Reflections(R-Work) 1498
    R-Factor(R-Work) 0.2804
    R-Factor(R-Free) 0.3203
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0311
    Shell Resolution(Low) 2.0602
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 1528
    R-Factor(R-Work) 0.2711
    R-Factor(R-Free) 0.3323
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0602
    Shell Resolution(Low) 2.0909
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1542
    R-Factor(R-Work) 0.2769
    R-Factor(R-Free) 0.283
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0909
    Shell Resolution(Low) 2.1236
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1536
    R-Factor(R-Work) 0.2516
    R-Factor(R-Free) 0.3035
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1236
    Shell Resolution(Low) 2.1584
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1639
    R-Factor(R-Work) 0.2452
    R-Factor(R-Free) 0.3006
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1584
    Shell Resolution(Low) 2.1956
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 1571
    R-Factor(R-Work) 0.2367
    R-Factor(R-Free) 0.2824
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1956
    Shell Resolution(Low) 2.2355
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1628
    R-Factor(R-Work) 0.2215
    R-Factor(R-Free) 0.2533
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2355
    Shell Resolution(Low) 2.2785
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 1613
    R-Factor(R-Work) 0.2226
    R-Factor(R-Free) 0.2328
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2785
    Shell Resolution(Low) 2.325
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1642
    R-Factor(R-Work) 0.2093
    R-Factor(R-Free) 0.2675
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.325
    Shell Resolution(Low) 2.3755
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 1637
    R-Factor(R-Work) 0.1998
    R-Factor(R-Free) 0.2667
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3755
    Shell Resolution(Low) 2.4307
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1661
    R-Factor(R-Work) 0.2062
    R-Factor(R-Free) 0.2466
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4307
    Shell Resolution(Low) 2.4915
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 1661
    R-Factor(R-Work) 0.1978
    R-Factor(R-Free) 0.2467
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4915
    Shell Resolution(Low) 2.5588
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 1700
    R-Factor(R-Work) 0.1864
    R-Factor(R-Free) 0.214
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5588
    Shell Resolution(Low) 2.6341
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1655
    R-Factor(R-Work) 0.1973
    R-Factor(R-Free) 0.2229
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6341
    Shell Resolution(Low) 2.719
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1647
    R-Factor(R-Work) 0.2031
    R-Factor(R-Free) 0.2575
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.719
    Shell Resolution(Low) 2.8161
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1694
    R-Factor(R-Work) 0.1903
    R-Factor(R-Free) 0.1957
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8161
    Shell Resolution(Low) 2.9288
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 1645
    R-Factor(R-Work) 0.1853
    R-Factor(R-Free) 0.2139
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9288
    Shell Resolution(Low) 3.062
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1694
    R-Factor(R-Work) 0.1867
    R-Factor(R-Free) 0.2186
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.062
    Shell Resolution(Low) 3.2232
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1677
    R-Factor(R-Work) 0.1851
    R-Factor(R-Free) 0.1928
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2232
    Shell Resolution(Low) 3.4249
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1692
    R-Factor(R-Work) 0.1786
    R-Factor(R-Free) 0.2066
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4249
    Shell Resolution(Low) 3.6889
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 1680
    R-Factor(R-Work) 0.1584
    R-Factor(R-Free) 0.1691
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6889
    Shell Resolution(Low) 4.0593
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 1718
    R-Factor(R-Work) 0.1603
    R-Factor(R-Free) 0.1699
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0593
    Shell Resolution(Low) 4.6448
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 1694
    R-Factor(R-Work) 0.1474
    R-Factor(R-Free) 0.1507
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6448
    Shell Resolution(Low) 5.8447
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 1694
    R-Factor(R-Work) 0.1687
    R-Factor(R-Free) 0.1951
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8447
    Shell Resolution(Low) 29.8027
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1748
    R-Factor(R-Work) 0.1857
    R-Factor(R-Free) 0.1816
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.002
    f_chiral_restr 0.046
    f_dihedral_angle_d 18.478
    f_angle_d 0.687
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3164
    Nucleic Acid Atoms 720
    Heterogen Atoms 4
    Solvent Atoms 423
     
     
  •   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: 1.8.1_1168)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.1_1168)
    model building AMoRE
    data collection HKL-2000