POP-OUT | CLOSE

An Information Portal to 107049 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DV3
  •   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 = 402.98 α = 90
    b = 402.98 β = 90
    c = 172.61 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 2010-04-19
     
    Diffraction Radiation
    Monochromator single crystal Si(220) side-bounce
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-E
    Wavelength List 0.98
    Site APS
    Beamline 24-ID-E
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.55
    Resolution(Low) 30
    Number Reflections(All) 164584
    Number Reflections(Observed) 164584
    Percent Possible(Observed) 96.6
    R Merge I(Observed) 0.156
    Redundancy 2.8
     
    High Resolution Shell Details
    Resolution(High) 3.546
    Resolution(Low) 3.68
    Percent Possible(All) 90.9
    R Merge I(Observed) 0.77
    Redundancy 2.6
    Number Unique Reflections(All) 15278
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.547
    Resolution(Low) 29.752
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 164335
    Number of Reflections(Observed) 164335
    Number of Reflections(R-Free) 8254
    Percent Reflections(Observed) 96.52
    R-Factor(Observed) 0.1689
    R-Work 0.1661
    R-Free 0.2202
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 152.503
    Anisotropic B[1][1] -17.4238
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -17.4238
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 21.6558
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.547
    Shell Resolution(Low) 3.5875
    Number of Reflections(R-Free) 269
    Number of Reflections(R-Work) 4746
    R-Factor(R-Work) 0.2799
    R-Factor(R-Free) 0.3285
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5875
    Shell Resolution(Low) 3.6296
    Number of Reflections(R-Free) 266
    Number of Reflections(R-Work) 4839
    R-Factor(R-Work) 0.2611
    R-Factor(R-Free) 0.2832
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6296
    Shell Resolution(Low) 3.6738
    Number of Reflections(R-Free) 259
    Number of Reflections(R-Work) 4871
    R-Factor(R-Work) 0.2539
    R-Factor(R-Free) 0.3224
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6738
    Shell Resolution(Low) 3.7202
    Number of Reflections(R-Free) 274
    Number of Reflections(R-Work) 4961
    R-Factor(R-Work) 0.2359
    R-Factor(R-Free) 0.3095
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7202
    Shell Resolution(Low) 3.769
    Number of Reflections(R-Free) 304
    Number of Reflections(R-Work) 5015
    R-Factor(R-Work) 0.223
    R-Factor(R-Free) 0.2619
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.769
    Shell Resolution(Low) 3.8206
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 5094
    R-Factor(R-Work) 0.2283
    R-Factor(R-Free) 0.2838
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8206
    Shell Resolution(Low) 3.875
    Number of Reflections(R-Free) 259
    Number of Reflections(R-Work) 5151
    R-Factor(R-Work) 0.2135
    R-Factor(R-Free) 0.262
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.875
    Shell Resolution(Low) 3.9328
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 5162
    R-Factor(R-Work) 0.2072
    R-Factor(R-Free) 0.2576
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9328
    Shell Resolution(Low) 3.9941
    Number of Reflections(R-Free) 281
    Number of Reflections(R-Work) 5196
    R-Factor(R-Work) 0.1964
    R-Factor(R-Free) 0.2503
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9941
    Shell Resolution(Low) 4.0594
    Number of Reflections(R-Free) 289
    Number of Reflections(R-Work) 5239
    R-Factor(R-Work) 0.1893
    R-Factor(R-Free) 0.2576
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0594
    Shell Resolution(Low) 4.1292
    Number of Reflections(R-Free) 312
    Number of Reflections(R-Work) 5226
    R-Factor(R-Work) 0.1873
    R-Factor(R-Free) 0.2296
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1292
    Shell Resolution(Low) 4.2041
    Number of Reflections(R-Free) 259
    Number of Reflections(R-Work) 5318
    R-Factor(R-Work) 0.1725
    R-Factor(R-Free) 0.2607
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2041
    Shell Resolution(Low) 4.2847
    Number of Reflections(R-Free) 261
    Number of Reflections(R-Work) 5309
    R-Factor(R-Work) 0.1674
    R-Factor(R-Free) 0.2242
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2847
    Shell Resolution(Low) 4.3719
    Number of Reflections(R-Free) 299
    Number of Reflections(R-Work) 5247
    R-Factor(R-Work) 0.168
    R-Factor(R-Free) 0.231
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3719
    Shell Resolution(Low) 4.4667
    Number of Reflections(R-Free) 307
    Number of Reflections(R-Work) 5272
    R-Factor(R-Work) 0.1591
    R-Factor(R-Free) 0.2028
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4667
    Shell Resolution(Low) 4.5702
    Number of Reflections(R-Free) 282
    Number of Reflections(R-Work) 5327
    R-Factor(R-Work) 0.1489
    R-Factor(R-Free) 0.1981
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5702
    Shell Resolution(Low) 4.6841
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 5356
    R-Factor(R-Work) 0.1447
    R-Factor(R-Free) 0.2023
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6841
    Shell Resolution(Low) 4.8102
    Number of Reflections(R-Free) 272
    Number of Reflections(R-Work) 5325
    R-Factor(R-Work) 0.1434
    R-Factor(R-Free) 0.21
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8102
    Shell Resolution(Low) 4.9512
    Number of Reflections(R-Free) 290
    Number of Reflections(R-Work) 5309
    R-Factor(R-Work) 0.1326
    R-Factor(R-Free) 0.1818
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9512
    Shell Resolution(Low) 5.1102
    Number of Reflections(R-Free) 269
    Number of Reflections(R-Work) 5326
    R-Factor(R-Work) 0.1382
    R-Factor(R-Free) 0.2052
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1102
    Shell Resolution(Low) 5.2919
    Number of Reflections(R-Free) 274
    Number of Reflections(R-Work) 5318
    R-Factor(R-Work) 0.134
    R-Factor(R-Free) 0.1983
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2919
    Shell Resolution(Low) 5.5025
    Number of Reflections(R-Free) 280
    Number of Reflections(R-Work) 5314
    R-Factor(R-Work) 0.1257
    R-Factor(R-Free) 0.1806
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5025
    Shell Resolution(Low) 5.7512
    Number of Reflections(R-Free) 285
    Number of Reflections(R-Work) 5312
    R-Factor(R-Work) 0.1371
    R-Factor(R-Free) 0.2103
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7512
    Shell Resolution(Low) 6.052
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 5310
    R-Factor(R-Work) 0.1424
    R-Factor(R-Free) 0.2088
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.052
    Shell Resolution(Low) 6.4276
    Number of Reflections(R-Free) 271
    Number of Reflections(R-Work) 5315
    R-Factor(R-Work) 0.1404
    R-Factor(R-Free) 0.1943
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.4276
    Shell Resolution(Low) 6.9181
    Number of Reflections(R-Free) 272
    Number of Reflections(R-Work) 5303
    R-Factor(R-Work) 0.1423
    R-Factor(R-Free) 0.2173
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.9181
    Shell Resolution(Low) 7.6038
    Number of Reflections(R-Free) 289
    Number of Reflections(R-Work) 5245
    R-Factor(R-Work) 0.1356
    R-Factor(R-Free) 0.2027
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.6038
    Shell Resolution(Low) 8.6801
    Number of Reflections(R-Free) 271
    Number of Reflections(R-Work) 5262
    R-Factor(R-Work) 0.1419
    R-Factor(R-Free) 0.1979
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.6801
    Shell Resolution(Low) 10.8472
    Number of Reflections(R-Free) 280
    Number of Reflections(R-Work) 5262
    R-Factor(R-Work) 0.1529
    R-Factor(R-Free) 0.1919
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.8472
    Shell Resolution(Low) 29.7533
    Number of Reflections(R-Free) 291
    Number of Reflections(R-Work) 5151
    R-Factor(R-Work) 0.2073
    R-Factor(R-Free) 0.2301
    Percent Reflections(Observed) 90.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 19.822
    f_plane_restr 0.009
    f_chiral_restr 0.09
    f_angle_d 1.598
    f_bond_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19088
    Nucleic Acid Atoms 32509
    Heterogen Atoms 323
    Solvent Atoms 382
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    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 SCALEPACK
    data collection DENZO