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X-RAY DIFFRACTION
Materials and Methods page
4LF4
  •   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 = 400.61 α = 90
    b = 400.61 β = 90
    c = 175.95 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 CCD
    Type ADSC QUANTUM 315
    Collection Date 2010-11-07
     
    Diffraction Radiation
    Monochromator KOHZU HLD8-24
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.98
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.34
    Resolution(Low) 35
    Number Reflections(All) 202709
    Number Reflections(Observed) 202709
    Percent Possible(Observed) 99.1
    R Merge I(Observed) 0.096
    Redundancy 3.2
     
    High Resolution Shell Details
    Resolution(High) 3.342
    Resolution(Low) 3.47
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.802
    Redundancy 3.2
    Number Unique Reflections(All) 20193
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.3421
    Resolution(Low) 34.352
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 202592
    Number of Reflections(Observed) 202592
    Number of Reflections(R-Free) 10183
    Percent Reflections(Observed) 98.92
    R-Factor(All) 0.1737
    R-Factor(Observed) 0.1737
    R-Work 0.1719
    R-Free 0.2077
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 114.001
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3421
    Shell Resolution(Low) 3.3801
    Number of Reflections(R-Free) 312
    Number of Reflections(R-Work) 6094
    R-Factor(R-Work) 0.2911
    R-Factor(R-Free) 0.3406
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3801
    Shell Resolution(Low) 3.4198
    Number of Reflections(R-Free) 349
    Number of Reflections(R-Work) 6426
    R-Factor(R-Work) 0.2778
    R-Factor(R-Free) 0.3082
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4198
    Shell Resolution(Low) 3.4615
    Number of Reflections(R-Free) 359
    Number of Reflections(R-Work) 6361
    R-Factor(R-Work) 0.2772
    R-Factor(R-Free) 0.2989
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4615
    Shell Resolution(Low) 3.5052
    Number of Reflections(R-Free) 351
    Number of Reflections(R-Work) 6403
    R-Factor(R-Work) 0.2599
    R-Factor(R-Free) 0.291
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5052
    Shell Resolution(Low) 3.5513
    Number of Reflections(R-Free) 393
    Number of Reflections(R-Work) 6371
    R-Factor(R-Work) 0.2492
    R-Factor(R-Free) 0.2877
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5513
    Shell Resolution(Low) 3.5999
    Number of Reflections(R-Free) 327
    Number of Reflections(R-Work) 6424
    R-Factor(R-Work) 0.2366
    R-Factor(R-Free) 0.2572
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5999
    Shell Resolution(Low) 3.6513
    Number of Reflections(R-Free) 328
    Number of Reflections(R-Work) 6423
    R-Factor(R-Work) 0.222
    R-Factor(R-Free) 0.2668
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6513
    Shell Resolution(Low) 3.7057
    Number of Reflections(R-Free) 369
    Number of Reflections(R-Work) 6382
    R-Factor(R-Work) 0.2115
    R-Factor(R-Free) 0.2258
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7057
    Shell Resolution(Low) 3.7636
    Number of Reflections(R-Free) 350
    Number of Reflections(R-Work) 6372
    R-Factor(R-Work) 0.1963
    R-Factor(R-Free) 0.2223
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7636
    Shell Resolution(Low) 3.8252
    Number of Reflections(R-Free) 304
    Number of Reflections(R-Work) 6496
    R-Factor(R-Work) 0.1871
    R-Factor(R-Free) 0.2219
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8252
    Shell Resolution(Low) 3.8911
    Number of Reflections(R-Free) 341
    Number of Reflections(R-Work) 6413
    R-Factor(R-Work) 0.1793
    R-Factor(R-Free) 0.2299
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8911
    Shell Resolution(Low) 3.9617
    Number of Reflections(R-Free) 322
    Number of Reflections(R-Work) 6434
    R-Factor(R-Work) 0.1767
    R-Factor(R-Free) 0.1928
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9617
    Shell Resolution(Low) 4.0378
    Number of Reflections(R-Free) 365
    Number of Reflections(R-Work) 6438
    R-Factor(R-Work) 0.1731
    R-Factor(R-Free) 0.2211
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0378
    Shell Resolution(Low) 4.1201
    Number of Reflections(R-Free) 363
    Number of Reflections(R-Work) 6394
    R-Factor(R-Work) 0.1637
    R-Factor(R-Free) 0.2055
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1201
    Shell Resolution(Low) 4.2095
    Number of Reflections(R-Free) 322
    Number of Reflections(R-Work) 6473
    R-Factor(R-Work) 0.1554
    R-Factor(R-Free) 0.1922
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2095
    Shell Resolution(Low) 4.3073
    Number of Reflections(R-Free) 337
    Number of Reflections(R-Work) 6453
    R-Factor(R-Work) 0.1511
    R-Factor(R-Free) 0.2011
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3073
    Shell Resolution(Low) 4.4148
    Number of Reflections(R-Free) 367
    Number of Reflections(R-Work) 6409
    R-Factor(R-Work) 0.1458
    R-Factor(R-Free) 0.1775
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4148
    Shell Resolution(Low) 4.5339
    Number of Reflections(R-Free) 353
    Number of Reflections(R-Work) 6427
    R-Factor(R-Work) 0.1463
    R-Factor(R-Free) 0.1775
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5339
    Shell Resolution(Low) 4.667
    Number of Reflections(R-Free) 313
    Number of Reflections(R-Work) 6478
    R-Factor(R-Work) 0.1441
    R-Factor(R-Free) 0.1949
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.667
    Shell Resolution(Low) 4.8172
    Number of Reflections(R-Free) 309
    Number of Reflections(R-Work) 6465
    R-Factor(R-Work) 0.1441
    R-Factor(R-Free) 0.196
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8172
    Shell Resolution(Low) 4.9889
    Number of Reflections(R-Free) 354
    Number of Reflections(R-Work) 6430
    R-Factor(R-Work) 0.1343
    R-Factor(R-Free) 0.1822
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9889
    Shell Resolution(Low) 5.188
    Number of Reflections(R-Free) 326
    Number of Reflections(R-Work) 6482
    R-Factor(R-Work) 0.1315
    R-Factor(R-Free) 0.1564
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.188
    Shell Resolution(Low) 5.4232
    Number of Reflections(R-Free) 321
    Number of Reflections(R-Work) 6462
    R-Factor(R-Work) 0.1325
    R-Factor(R-Free) 0.1827
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4232
    Shell Resolution(Low) 5.7079
    Number of Reflections(R-Free) 351
    Number of Reflections(R-Work) 6457
    R-Factor(R-Work) 0.1335
    R-Factor(R-Free) 0.1644
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7079
    Shell Resolution(Low) 6.0637
    Number of Reflections(R-Free) 325
    Number of Reflections(R-Work) 6482
    R-Factor(R-Work) 0.1393
    R-Factor(R-Free) 0.1831
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0637
    Shell Resolution(Low) 6.529
    Number of Reflections(R-Free) 329
    Number of Reflections(R-Work) 6459
    R-Factor(R-Work) 0.1477
    R-Factor(R-Free) 0.1957
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.529
    Shell Resolution(Low) 7.1806
    Number of Reflections(R-Free) 337
    Number of Reflections(R-Work) 6421
    R-Factor(R-Work) 0.1458
    R-Factor(R-Free) 0.1847
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1806
    Shell Resolution(Low) 8.2073
    Number of Reflections(R-Free) 323
    Number of Reflections(R-Work) 6401
    R-Factor(R-Work) 0.1513
    R-Factor(R-Free) 0.1907
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.2073
    Shell Resolution(Low) 10.2939
    Number of Reflections(R-Free) 352
    Number of Reflections(R-Work) 6412
    R-Factor(R-Work) 0.1806
    R-Factor(R-Free) 0.204
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.2939
    Shell Resolution(Low) 34.3537
    Number of Reflections(R-Free) 331
    Number of Reflections(R-Work) 6267
    R-Factor(R-Work) 0.217
    R-Factor(R-Free) 0.234
    Percent Reflections(Observed) 91.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 16.137
    f_plane_restr 0.004
    f_chiral_restr 0.049
    f_angle_d 0.816
    f_bond_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19153
    Nucleic Acid Atoms 32522
    Heterogen Atoms 196
    Solvent Atoms 6
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: dev_1119)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK
    data collection DENZO