POP-OUT | CLOSE

An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4IL0
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 4.6
    Temperature 282.0
    Details Protein solution was at 20 mg/mL containing 50 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME. Mother liqueur contained 0.2 M Na citrate (pH 4.6), 20% PEG 3,350. 20% glycerol was used as the cryoprotectant, vapor diffusion, hanging drop, temperature 282K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 86.09 α = 101.47
    b = 94.03 β = 96.74
    c = 155.2 γ = 79.86
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-300
    Collection Date 2012-12-12
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-D
    Wavelength List 0.978590
    Site APS
    Beamline 21-ID-D
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.8
    Resolution(Low) 30
    Number Reflections(All) 115292
    Number Reflections(Observed) 112207
    Percent Possible(Observed) 97.3
    R Merge I(Observed) 0.143
    B(Isotropic) From Wilson Plot 36.789
     
    High Resolution Shell Details
    Resolution(High) 2.8
    Resolution(Low) 2.87
    Percent Possible(All) 97.8
    R Merge I(Observed) 0.539
    Mean I Over Sigma(Observed) 2.33
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.8
    Resolution(Low) 19.86
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 115249
    Number of Reflections(Observed) 112188
    Number of Reflections(R-Free) 5609
    Percent Reflections(Observed) 97.61
    R-Factor(All) 0.226
    R-Factor(Observed) 0.1762
    R-Work 0.1733
    R-Free 0.2313
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 27.6265
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7999
    Shell Resolution(Low) 2.8316
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3595
    R-Factor(R-Work) 0.2433
    R-Factor(R-Free) 0.2965
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8316
    Shell Resolution(Low) 2.8649
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3555
    R-Factor(R-Work) 0.2442
    R-Factor(R-Free) 0.3113
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8649
    Shell Resolution(Low) 2.8997
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3549
    R-Factor(R-Work) 0.2381
    R-Factor(R-Free) 0.3224
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8997
    Shell Resolution(Low) 2.9363
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3575
    R-Factor(R-Work) 0.2504
    R-Factor(R-Free) 0.3342
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9363
    Shell Resolution(Low) 2.9748
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3535
    R-Factor(R-Work) 0.2525
    R-Factor(R-Free) 0.3416
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9748
    Shell Resolution(Low) 3.0154
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3537
    R-Factor(R-Work) 0.2359
    R-Factor(R-Free) 0.3175
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0154
    Shell Resolution(Low) 3.0583
    Number of Reflections(R-Free) 190
    Number of Reflections(R-Work) 3610
    R-Factor(R-Work) 0.2318
    R-Factor(R-Free) 0.2951
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0583
    Shell Resolution(Low) 3.1038
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3511
    R-Factor(R-Work) 0.2165
    R-Factor(R-Free) 0.3041
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1038
    Shell Resolution(Low) 3.1521
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3572
    R-Factor(R-Work) 0.2157
    R-Factor(R-Free) 0.283
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1521
    Shell Resolution(Low) 3.2036
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3545
    R-Factor(R-Work) 0.2093
    R-Factor(R-Free) 0.274
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2036
    Shell Resolution(Low) 3.2586
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3542
    R-Factor(R-Work) 0.2024
    R-Factor(R-Free) 0.2852
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2586
    Shell Resolution(Low) 3.3176
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3568
    R-Factor(R-Work) 0.1999
    R-Factor(R-Free) 0.2788
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3176
    Shell Resolution(Low) 3.3811
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3555
    R-Factor(R-Work) 0.1884
    R-Factor(R-Free) 0.2621
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3811
    Shell Resolution(Low) 3.4498
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3582
    R-Factor(R-Work) 0.1855
    R-Factor(R-Free) 0.2656
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4498
    Shell Resolution(Low) 3.5244
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3487
    R-Factor(R-Work) 0.1855
    R-Factor(R-Free) 0.2314
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5244
    Shell Resolution(Low) 3.6059
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3564
    R-Factor(R-Work) 0.1801
    R-Factor(R-Free) 0.254
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6059
    Shell Resolution(Low) 3.6955
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3541
    R-Factor(R-Work) 0.1702
    R-Factor(R-Free) 0.2146
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6955
    Shell Resolution(Low) 3.7948
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3554
    R-Factor(R-Work) 0.1603
    R-Factor(R-Free) 0.2309
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7948
    Shell Resolution(Low) 3.9056
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3552
    R-Factor(R-Work) 0.1544
    R-Factor(R-Free) 0.1968
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9056
    Shell Resolution(Low) 4.0307
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3515
    R-Factor(R-Work) 0.1453
    R-Factor(R-Free) 0.1907
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0307
    Shell Resolution(Low) 4.1734
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3536
    R-Factor(R-Work) 0.1492
    R-Factor(R-Free) 0.2299
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1734
    Shell Resolution(Low) 4.3389
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3563
    R-Factor(R-Work) 0.1426
    R-Factor(R-Free) 0.1872
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3389
    Shell Resolution(Low) 4.5341
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3579
    R-Factor(R-Work) 0.1345
    R-Factor(R-Free) 0.2031
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5341
    Shell Resolution(Low) 4.77
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3556
    R-Factor(R-Work) 0.1326
    R-Factor(R-Free) 0.1834
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.77
    Shell Resolution(Low) 5.0642
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3558
    R-Factor(R-Work) 0.129
    R-Factor(R-Free) 0.1683
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0642
    Shell Resolution(Low) 5.4478
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3546
    R-Factor(R-Work) 0.1382
    R-Factor(R-Free) 0.1995
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4478
    Shell Resolution(Low) 5.9824
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3553
    R-Factor(R-Work) 0.1632
    R-Factor(R-Free) 0.2011
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9824
    Shell Resolution(Low) 6.8172
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3556
    R-Factor(R-Work) 0.1627
    R-Factor(R-Free) 0.2276
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.8172
    Shell Resolution(Low) 8.4763
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3578
    R-Factor(R-Work) 0.1512
    R-Factor(R-Free) 0.1693
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.4763
    Shell Resolution(Low) 19.8607
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3510
    R-Factor(R-Work) 0.15
    R-Factor(R-Free) 0.18
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.787
    f_plane_restr 0.007
    f_chiral_restr 0.074
    f_angle_d 1.253
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 26575
    Nucleic Acid Atoms 0
    Heterogen Atoms 116
    Solvent Atoms 481
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-3000
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8_1066)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction Xscale