POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4LFC
  •   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 = 401.83 α = 90
    b = 401.83 β = 90
    c = 175.89 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) 3.6
    Resolution(Low) 35
    Number Reflections(All) 163923
    Number Reflections(Observed) 163923
    Percent Possible(Observed) 99.4
    R Merge I(Observed) 0.086
    Redundancy 3.3
     
    High Resolution Shell Details
    Resolution(High) 3.6
    Resolution(Low) 3.73
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.789
    Redundancy 3.3
    Number Unique Reflections(All) 16240
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.602
    Resolution(Low) 34.457
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 163849
    Number of Reflections(Observed) 163849
    Number of Reflections(R-Free) 8182
    Percent Reflections(Observed) 99.36
    R-Factor(All) 0.1651
    R-Factor(Observed) 0.1651
    R-Work 0.1628
    R-Free 0.2089
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 133.258
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.602
    Shell Resolution(Low) 3.6429
    Number of Reflections(R-Free) 251
    Number of Reflections(R-Work) 5127
    R-Factor(R-Work) 0.2824
    R-Factor(R-Free) 0.329
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6429
    Shell Resolution(Low) 3.6857
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 5153
    R-Factor(R-Work) 0.2558
    R-Factor(R-Free) 0.2862
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6857
    Shell Resolution(Low) 3.7306
    Number of Reflections(R-Free) 290
    Number of Reflections(R-Work) 5110
    R-Factor(R-Work) 0.2416
    R-Factor(R-Free) 0.2983
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7306
    Shell Resolution(Low) 3.7778
    Number of Reflections(R-Free) 295
    Number of Reflections(R-Work) 5123
    R-Factor(R-Work) 0.2362
    R-Factor(R-Free) 0.2933
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7778
    Shell Resolution(Low) 3.8274
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 5238
    R-Factor(R-Work) 0.2256
    R-Factor(R-Free) 0.2891
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8274
    Shell Resolution(Low) 3.8798
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 5189
    R-Factor(R-Work) 0.2047
    R-Factor(R-Free) 0.2668
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8798
    Shell Resolution(Low) 3.9352
    Number of Reflections(R-Free) 301
    Number of Reflections(R-Work) 5105
    R-Factor(R-Work) 0.1971
    R-Factor(R-Free) 0.2368
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9352
    Shell Resolution(Low) 3.9938
    Number of Reflections(R-Free) 251
    Number of Reflections(R-Work) 5229
    R-Factor(R-Work) 0.1888
    R-Factor(R-Free) 0.2285
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9938
    Shell Resolution(Low) 4.0561
    Number of Reflections(R-Free) 289
    Number of Reflections(R-Work) 5131
    R-Factor(R-Work) 0.1895
    R-Factor(R-Free) 0.2379
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0561
    Shell Resolution(Low) 4.1225
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 5150
    R-Factor(R-Work) 0.1722
    R-Factor(R-Free) 0.2271
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1225
    Shell Resolution(Low) 4.1935
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 5183
    R-Factor(R-Work) 0.164
    R-Factor(R-Free) 0.2327
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1935
    Shell Resolution(Low) 4.2696
    Number of Reflections(R-Free) 270
    Number of Reflections(R-Work) 5166
    R-Factor(R-Work) 0.1574
    R-Factor(R-Free) 0.2162
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2696
    Shell Resolution(Low) 4.3516
    Number of Reflections(R-Free) 287
    Number of Reflections(R-Work) 5137
    R-Factor(R-Work) 0.147
    R-Factor(R-Free) 0.2026
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3516
    Shell Resolution(Low) 4.4402
    Number of Reflections(R-Free) 271
    Number of Reflections(R-Work) 5165
    R-Factor(R-Work) 0.1435
    R-Factor(R-Free) 0.1859
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4402
    Shell Resolution(Low) 4.5366
    Number of Reflections(R-Free) 308
    Number of Reflections(R-Work) 5141
    R-Factor(R-Work) 0.1403
    R-Factor(R-Free) 0.187
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5366
    Shell Resolution(Low) 4.6418
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 5203
    R-Factor(R-Work) 0.1297
    R-Factor(R-Free) 0.1719
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6418
    Shell Resolution(Low) 4.7576
    Number of Reflections(R-Free) 248
    Number of Reflections(R-Work) 5212
    R-Factor(R-Work) 0.13
    R-Factor(R-Free) 0.1836
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7576
    Shell Resolution(Low) 4.8859
    Number of Reflections(R-Free) 260
    Number of Reflections(R-Work) 5187
    R-Factor(R-Work) 0.1319
    R-Factor(R-Free) 0.1968
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8859
    Shell Resolution(Low) 5.0293
    Number of Reflections(R-Free) 291
    Number of Reflections(R-Work) 5200
    R-Factor(R-Work) 0.1298
    R-Factor(R-Free) 0.1889
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0293
    Shell Resolution(Low) 5.1911
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 5174
    R-Factor(R-Work) 0.1228
    R-Factor(R-Free) 0.1603
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1911
    Shell Resolution(Low) 5.376
    Number of Reflections(R-Free) 262
    Number of Reflections(R-Work) 5188
    R-Factor(R-Work) 0.1223
    R-Factor(R-Free) 0.1713
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.376
    Shell Resolution(Low) 5.5903
    Number of Reflections(R-Free) 283
    Number of Reflections(R-Work) 5224
    R-Factor(R-Work) 0.1239
    R-Factor(R-Free) 0.18
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5903
    Shell Resolution(Low) 5.8436
    Number of Reflections(R-Free) 278
    Number of Reflections(R-Work) 5235
    R-Factor(R-Work) 0.1246
    R-Factor(R-Free) 0.1795
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8436
    Shell Resolution(Low) 6.15
    Number of Reflections(R-Free) 249
    Number of Reflections(R-Work) 5247
    R-Factor(R-Work) 0.1272
    R-Factor(R-Free) 0.1827
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.15
    Shell Resolution(Low) 6.5329
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 5272
    R-Factor(R-Work) 0.1292
    R-Factor(R-Free) 0.1731
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5329
    Shell Resolution(Low) 7.0334
    Number of Reflections(R-Free) 275
    Number of Reflections(R-Work) 5246
    R-Factor(R-Work) 0.1315
    R-Factor(R-Free) 0.172
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.0334
    Shell Resolution(Low) 7.7339
    Number of Reflections(R-Free) 277
    Number of Reflections(R-Work) 5247
    R-Factor(R-Work) 0.136
    R-Factor(R-Free) 0.178
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.7339
    Shell Resolution(Low) 8.8365
    Number of Reflections(R-Free) 277
    Number of Reflections(R-Work) 5261
    R-Factor(R-Work) 0.1482
    R-Factor(R-Free) 0.2017
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.8365
    Shell Resolution(Low) 11.0714
    Number of Reflections(R-Free) 279
    Number of Reflections(R-Work) 5248
    R-Factor(R-Work) 0.1762
    R-Factor(R-Free) 0.1989
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 11.0714
    Shell Resolution(Low) 34.4583
    Number of Reflections(R-Free) 285
    Number of Reflections(R-Work) 5176
    R-Factor(R-Work) 0.2335
    R-Factor(R-Free) 0.2601
    Percent Reflections(Observed) 93.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.259
    f_plane_restr 0.006
    f_chiral_restr 0.068
    f_angle_d 1.425
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19153
    Nucleic Acid Atoms 32504
    Heterogen Atoms 183
    Solvent Atoms 48
     
     
  •   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