POP-OUT | CLOSE

An Information Portal to 110790 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4JI3
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 277.0
    Details MPD , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 402.98 α = 90
    b = 402.98 β = 90
    c = 173.12 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 Monochromator
    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) 3.35
    Resolution(Low) 35
    Number Reflections(All) 178536
    Number Reflections(Observed) 178536
    Percent Possible(Observed) 88.2
    R Merge I(Observed) 0.072
    Redundancy 4.4
     
    High Resolution Shell Details
    Resolution(High) 3.35
    Resolution(Low) 3.47
    Percent Possible(All) 92.3
    R Merge I(Observed) 0.624
    Redundancy 4.3
    Number Unique Reflections(All) 18472
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.35
    Resolution(Low) 34.002
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 178313
    Number of Reflections(Observed) 178313
    Number of Reflections(R-Free) 8991
    Percent Reflections(Observed) 87.75
    R-Factor(Observed) 0.1701
    R-Work 0.1677
    R-Free 0.2152
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 144.32
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3461
    Shell Resolution(Low) 3.3841
    Number of Reflections(R-Free) 278
    Number of Reflections(R-Work) 5150
    R-Factor(R-Work) 0.2853
    R-Factor(R-Free) 0.3387
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3841
    Shell Resolution(Low) 3.4239
    Number of Reflections(R-Free) 346
    Number of Reflections(R-Work) 5851
    R-Factor(R-Work) 0.2716
    R-Factor(R-Free) 0.334
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4239
    Shell Resolution(Low) 3.4656
    Number of Reflections(R-Free) 324
    Number of Reflections(R-Work) 5831
    R-Factor(R-Work) 0.2631
    R-Factor(R-Free) 0.2976
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4656
    Shell Resolution(Low) 3.5095
    Number of Reflections(R-Free) 340
    Number of Reflections(R-Work) 5830
    R-Factor(R-Work) 0.2483
    R-Factor(R-Free) 0.2974
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5095
    Shell Resolution(Low) 3.5556
    Number of Reflections(R-Free) 324
    Number of Reflections(R-Work) 5799
    R-Factor(R-Work) 0.2403
    R-Factor(R-Free) 0.2823
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5556
    Shell Resolution(Low) 3.6042
    Number of Reflections(R-Free) 318
    Number of Reflections(R-Work) 5852
    R-Factor(R-Work) 0.226
    R-Factor(R-Free) 0.2436
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6042
    Shell Resolution(Low) 3.6557
    Number of Reflections(R-Free) 301
    Number of Reflections(R-Work) 5822
    R-Factor(R-Work) 0.2218
    R-Factor(R-Free) 0.2686
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6557
    Shell Resolution(Low) 3.7102
    Number of Reflections(R-Free) 317
    Number of Reflections(R-Work) 5772
    R-Factor(R-Work) 0.2191
    R-Factor(R-Free) 0.2861
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7102
    Shell Resolution(Low) 3.7681
    Number of Reflections(R-Free) 330
    Number of Reflections(R-Work) 5796
    R-Factor(R-Work) 0.2078
    R-Factor(R-Free) 0.2584
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7681
    Shell Resolution(Low) 3.8298
    Number of Reflections(R-Free) 269
    Number of Reflections(R-Work) 5795
    R-Factor(R-Work) 0.2012
    R-Factor(R-Free) 0.2789
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8298
    Shell Resolution(Low) 3.8957
    Number of Reflections(R-Free) 294
    Number of Reflections(R-Work) 5772
    R-Factor(R-Work) 0.1944
    R-Factor(R-Free) 0.2209
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8957
    Shell Resolution(Low) 3.9665
    Number of Reflections(R-Free) 308
    Number of Reflections(R-Work) 5751
    R-Factor(R-Work) 0.1758
    R-Factor(R-Free) 0.2352
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9665
    Shell Resolution(Low) 4.0426
    Number of Reflections(R-Free) 321
    Number of Reflections(R-Work) 5734
    R-Factor(R-Work) 0.1722
    R-Factor(R-Free) 0.2297
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0426
    Shell Resolution(Low) 4.125
    Number of Reflections(R-Free) 322
    Number of Reflections(R-Work) 5717
    R-Factor(R-Work) 0.1683
    R-Factor(R-Free) 0.2166
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.125
    Shell Resolution(Low) 4.2145
    Number of Reflections(R-Free) 275
    Number of Reflections(R-Work) 5749
    R-Factor(R-Work) 0.1637
    R-Factor(R-Free) 0.2293
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2145
    Shell Resolution(Low) 4.3124
    Number of Reflections(R-Free) 292
    Number of Reflections(R-Work) 5683
    R-Factor(R-Work) 0.1624
    R-Factor(R-Free) 0.2311
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3124
    Shell Resolution(Low) 4.42
    Number of Reflections(R-Free) 297
    Number of Reflections(R-Work) 5708
    R-Factor(R-Work) 0.1651
    R-Factor(R-Free) 0.2061
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.42
    Shell Resolution(Low) 4.5393
    Number of Reflections(R-Free) 336
    Number of Reflections(R-Work) 5644
    R-Factor(R-Work) 0.1578
    R-Factor(R-Free) 0.2179
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5393
    Shell Resolution(Low) 4.6725
    Number of Reflections(R-Free) 284
    Number of Reflections(R-Work) 5674
    R-Factor(R-Work) 0.1507
    R-Factor(R-Free) 0.1927
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6725
    Shell Resolution(Low) 4.8229
    Number of Reflections(R-Free) 270
    Number of Reflections(R-Work) 5684
    R-Factor(R-Work) 0.1424
    R-Factor(R-Free) 0.1844
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8229
    Shell Resolution(Low) 4.9948
    Number of Reflections(R-Free) 311
    Number of Reflections(R-Work) 5576
    R-Factor(R-Work) 0.1349
    R-Factor(R-Free) 0.2042
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9948
    Shell Resolution(Low) 5.1941
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 5599
    R-Factor(R-Work) 0.1341
    R-Factor(R-Free) 0.1737
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1941
    Shell Resolution(Low) 5.4296
    Number of Reflections(R-Free) 281
    Number of Reflections(R-Work) 5611
    R-Factor(R-Work) 0.1353
    R-Factor(R-Free) 0.208
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4296
    Shell Resolution(Low) 5.7146
    Number of Reflections(R-Free) 308
    Number of Reflections(R-Work) 5535
    R-Factor(R-Work) 0.1427
    R-Factor(R-Free) 0.2038
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7146
    Shell Resolution(Low) 6.0707
    Number of Reflections(R-Free) 266
    Number of Reflections(R-Work) 5536
    R-Factor(R-Work) 0.1438
    R-Factor(R-Free) 0.1951
    Percent Reflections(Observed) 85.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0707
    Shell Resolution(Low) 6.5364
    Number of Reflections(R-Free) 277
    Number of Reflections(R-Work) 5485
    R-Factor(R-Work) 0.1472
    R-Factor(R-Free) 0.1951
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5364
    Shell Resolution(Low) 7.1886
    Number of Reflections(R-Free) 294
    Number of Reflections(R-Work) 5464
    R-Factor(R-Work) 0.1358
    R-Factor(R-Free) 0.1757
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1886
    Shell Resolution(Low) 8.2159
    Number of Reflections(R-Free) 270
    Number of Reflections(R-Work) 5415
    R-Factor(R-Work) 0.1417
    R-Factor(R-Free) 0.2017
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.2159
    Shell Resolution(Low) 10.3032
    Number of Reflections(R-Free) 302
    Number of Reflections(R-Work) 5322
    R-Factor(R-Work) 0.1584
    R-Factor(R-Free) 0.1891
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.3032
    Shell Resolution(Low) 34.0035
    Number of Reflections(R-Free) 272
    Number of Reflections(R-Work) 5165
    R-Factor(R-Work) 0.1877
    R-Factor(R-Free) 0.205
    Percent Reflections(Observed) 75.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.614
    f_plane_restr 0.005
    f_chiral_restr 0.06
    f_angle_d 1.034
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19093
    Nucleic Acid Atoms 32487
    Heterogen Atoms 288
    Solvent Atoms 233
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHENIX (phenix.refine: dev_1119)
    Structure Refinement PHENIX (phenix.refine: dev_1119)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK
    data collection DENZO