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X-RAY DIFFRACTION
Materials and Methods page
4DR6
  •   Crystallization Hide
    Crystallization Experiments
    Method HANGING DROP
    pH 6.5
    Temperature 277.0
    Details MPD, pH 6.5, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 402.6 α = 90
    b = 402.6 β = 90
    c = 174.9 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2011-06-28
     
    Diffraction Radiation
    Monochromator double crystal Si(111) monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X25
    Wavelength List 1.1
    Site NSLS
    Beamline X25
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.3
    Resolution(Low) 50
    Number Reflections(All) 213602
    Number Reflections(Observed) 213602
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.092
    B(Isotropic) From Wilson Plot 104.363
     
    High Resolution Shell Details
    Resolution(High) 3.3
    Resolution(Low) 3.39
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.012
    Mean I Over Sigma(Observed) 2.02
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.3
    Resolution(Low) 49.484
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 213574
    Number of Reflections(Observed) 213574
    Number of Reflections(R-Free) 10749
    Percent Reflections(Observed) 99.97
    R-Factor(Observed) 0.1554
    R-Work 0.1534
    R-Free 0.1918
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 120.824
    Anisotropic B[1][1] 2.4527
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 2.4527
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 10.6777
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3
    Shell Resolution(Low) 3.3374
    Number of Reflections(R-Free) 342
    Number of Reflections(R-Work) 6618
    R-Factor(R-Work) 0.2586
    R-Factor(R-Free) 0.3135
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3374
    Shell Resolution(Low) 3.3767
    Number of Reflections(R-Free) 384
    Number of Reflections(R-Work) 6717
    R-Factor(R-Work) 0.2393
    R-Factor(R-Free) 0.2607
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3767
    Shell Resolution(Low) 3.4178
    Number of Reflections(R-Free) 352
    Number of Reflections(R-Work) 6670
    R-Factor(R-Work) 0.2289
    R-Factor(R-Free) 0.2847
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4178
    Shell Resolution(Low) 3.4611
    Number of Reflections(R-Free) 339
    Number of Reflections(R-Work) 6712
    R-Factor(R-Work) 0.2159
    R-Factor(R-Free) 0.248
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4611
    Shell Resolution(Low) 3.5066
    Number of Reflections(R-Free) 366
    Number of Reflections(R-Work) 6697
    R-Factor(R-Work) 0.212
    R-Factor(R-Free) 0.2459
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5066
    Shell Resolution(Low) 3.5547
    Number of Reflections(R-Free) 352
    Number of Reflections(R-Work) 6698
    R-Factor(R-Work) 0.2087
    R-Factor(R-Free) 0.2537
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5547
    Shell Resolution(Low) 3.6054
    Number of Reflections(R-Free) 361
    Number of Reflections(R-Work) 6667
    R-Factor(R-Work) 0.2034
    R-Factor(R-Free) 0.2505
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6054
    Shell Resolution(Low) 3.6592
    Number of Reflections(R-Free) 383
    Number of Reflections(R-Work) 6709
    R-Factor(R-Work) 0.1867
    R-Factor(R-Free) 0.2542
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6592
    Shell Resolution(Low) 3.7164
    Number of Reflections(R-Free) 350
    Number of Reflections(R-Work) 6700
    R-Factor(R-Work) 0.1719
    R-Factor(R-Free) 0.2108
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7164
    Shell Resolution(Low) 3.7773
    Number of Reflections(R-Free) 361
    Number of Reflections(R-Work) 6704
    R-Factor(R-Work) 0.1636
    R-Factor(R-Free) 0.1989
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7773
    Shell Resolution(Low) 3.8424
    Number of Reflections(R-Free) 384
    Number of Reflections(R-Work) 6678
    R-Factor(R-Work) 0.1576
    R-Factor(R-Free) 0.1944
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8424
    Shell Resolution(Low) 3.9122
    Number of Reflections(R-Free) 356
    Number of Reflections(R-Work) 6709
    R-Factor(R-Work) 0.157
    R-Factor(R-Free) 0.1947
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9122
    Shell Resolution(Low) 3.9875
    Number of Reflections(R-Free) 340
    Number of Reflections(R-Work) 6764
    R-Factor(R-Work) 0.1519
    R-Factor(R-Free) 0.1875
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9875
    Shell Resolution(Low) 4.0688
    Number of Reflections(R-Free) 344
    Number of Reflections(R-Work) 6731
    R-Factor(R-Work) 0.1478
    R-Factor(R-Free) 0.1917
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0688
    Shell Resolution(Low) 4.1572
    Number of Reflections(R-Free) 345
    Number of Reflections(R-Work) 6727
    R-Factor(R-Work) 0.1436
    R-Factor(R-Free) 0.2089
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1572
    Shell Resolution(Low) 4.2539
    Number of Reflections(R-Free) 359
    Number of Reflections(R-Work) 6735
    R-Factor(R-Work) 0.14
    R-Factor(R-Free) 0.1851
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2539
    Shell Resolution(Low) 4.3602
    Number of Reflections(R-Free) 351
    Number of Reflections(R-Work) 6718
    R-Factor(R-Work) 0.1362
    R-Factor(R-Free) 0.1843
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3602
    Shell Resolution(Low) 4.478
    Number of Reflections(R-Free) 370
    Number of Reflections(R-Work) 6770
    R-Factor(R-Work) 0.1313
    R-Factor(R-Free) 0.1744
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.478
    Shell Resolution(Low) 4.6097
    Number of Reflections(R-Free) 316
    Number of Reflections(R-Work) 6777
    R-Factor(R-Work) 0.1283
    R-Factor(R-Free) 0.1828
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6097
    Shell Resolution(Low) 4.7584
    Number of Reflections(R-Free) 352
    Number of Reflections(R-Work) 6727
    R-Factor(R-Work) 0.1278
    R-Factor(R-Free) 0.1726
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7584
    Shell Resolution(Low) 4.9283
    Number of Reflections(R-Free) 332
    Number of Reflections(R-Work) 6793
    R-Factor(R-Work) 0.1201
    R-Factor(R-Free) 0.1738
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9283
    Shell Resolution(Low) 5.1254
    Number of Reflections(R-Free) 341
    Number of Reflections(R-Work) 6785
    R-Factor(R-Work) 0.1232
    R-Factor(R-Free) 0.1593
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1254
    Shell Resolution(Low) 5.3584
    Number of Reflections(R-Free) 382
    Number of Reflections(R-Work) 6749
    R-Factor(R-Work) 0.1322
    R-Factor(R-Free) 0.1712
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3584
    Shell Resolution(Low) 5.6406
    Number of Reflections(R-Free) 342
    Number of Reflections(R-Work) 6812
    R-Factor(R-Work) 0.1254
    R-Factor(R-Free) 0.1686
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6406
    Shell Resolution(Low) 5.9934
    Number of Reflections(R-Free) 390
    Number of Reflections(R-Work) 6785
    R-Factor(R-Work) 0.1223
    R-Factor(R-Free) 0.162
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9934
    Shell Resolution(Low) 6.4552
    Number of Reflections(R-Free) 344
    Number of Reflections(R-Work) 6839
    R-Factor(R-Work) 0.1277
    R-Factor(R-Free) 0.1814
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.4552
    Shell Resolution(Low) 7.1032
    Number of Reflections(R-Free) 347
    Number of Reflections(R-Work) 6864
    R-Factor(R-Work) 0.1249
    R-Factor(R-Free) 0.164
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1032
    Shell Resolution(Low) 8.1271
    Number of Reflections(R-Free) 370
    Number of Reflections(R-Work) 6866
    R-Factor(R-Work) 0.1264
    R-Factor(R-Free) 0.1569
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.1271
    Shell Resolution(Low) 10.2244
    Number of Reflections(R-Free) 399
    Number of Reflections(R-Work) 6933
    R-Factor(R-Work) 0.1541
    R-Factor(R-Free) 0.1869
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.2244
    Shell Resolution(Low) 49.4892
    Number of Reflections(R-Free) 395
    Number of Reflections(R-Work) 7171
    R-Factor(R-Work) 0.2062
    R-Factor(R-Free) 0.2168
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.616
    f_plane_restr 0.005
    f_chiral_restr 0.065
    f_angle_d 0.946
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19127
    Nucleic Acid Atoms 33097
    Heterogen Atoms 418
    Solvent Atoms 907
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) xds
    Data Reduction (data scaling) XSCALE
    Structure Solution PHENIX (phenix.refine: dev_978)
    Structure Refinement PHENIX (phenix.refine: dev_978)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    data reduction Xscale