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X-RAY DIFFRACTION
Materials and Methods page
4DV2
  •   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 = 403.74 α = 90
    b = 403.74 β = 90
    c = 173.22 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) 3.65
    Resolution(Low) 30
    Number Reflections(All) 153457
    Number Reflections(Observed) 153457
    Percent Possible(Observed) 97.2
    R Merge I(Observed) 0.12
    Redundancy 3.1
     
    High Resolution Shell Details
    Resolution(High) 3.646
    Resolution(Low) 3.78
    Percent Possible(All) 97.5
    R Merge I(Observed) 0.759
    Redundancy 3.1
    Number Unique Reflections(All) 15255
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.646
    Resolution(Low) 29.771
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 153299
    Number of Reflections(Observed) 153299
    Number of Reflections(R-Free) 7637
    Percent Reflections(Observed) 96.99
    R-Factor(Observed) 0.1675
    R-Work 0.1645
    R-Free 0.223
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 173.946
    Anisotropic B[1][1] -9.8508
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -9.8508
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 16.0687
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.646
    Shell Resolution(Low) 3.6876
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 4479
    R-Factor(R-Work) 0.2994
    R-Factor(R-Free) 0.336
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6876
    Shell Resolution(Low) 3.7309
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 4830
    R-Factor(R-Work) 0.2725
    R-Factor(R-Free) 0.3356
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7309
    Shell Resolution(Low) 3.7763
    Number of Reflections(R-Free) 287
    Number of Reflections(R-Work) 4822
    R-Factor(R-Work) 0.2521
    R-Factor(R-Free) 0.3128
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7763
    Shell Resolution(Low) 3.824
    Number of Reflections(R-Free) 214
    Number of Reflections(R-Work) 4906
    R-Factor(R-Work) 0.2504
    R-Factor(R-Free) 0.3082
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.824
    Shell Resolution(Low) 3.8743
    Number of Reflections(R-Free) 270
    Number of Reflections(R-Work) 4883
    R-Factor(R-Work) 0.2299
    R-Factor(R-Free) 0.2777
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8743
    Shell Resolution(Low) 3.9272
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 4900
    R-Factor(R-Work) 0.2296
    R-Factor(R-Free) 0.281
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9272
    Shell Resolution(Low) 3.9832
    Number of Reflections(R-Free) 249
    Number of Reflections(R-Work) 4862
    R-Factor(R-Work) 0.2178
    R-Factor(R-Free) 0.2863
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9832
    Shell Resolution(Low) 4.0425
    Number of Reflections(R-Free) 277
    Number of Reflections(R-Work) 4895
    R-Factor(R-Work) 0.2102
    R-Factor(R-Free) 0.253
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0425
    Shell Resolution(Low) 4.1055
    Number of Reflections(R-Free) 295
    Number of Reflections(R-Work) 4880
    R-Factor(R-Work) 0.2
    R-Factor(R-Free) 0.2611
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1055
    Shell Resolution(Low) 4.1727
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 4940
    R-Factor(R-Work) 0.1925
    R-Factor(R-Free) 0.2626
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1727
    Shell Resolution(Low) 4.2444
    Number of Reflections(R-Free) 239
    Number of Reflections(R-Work) 4926
    R-Factor(R-Work) 0.181
    R-Factor(R-Free) 0.2615
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2444
    Shell Resolution(Low) 4.3214
    Number of Reflections(R-Free) 276
    Number of Reflections(R-Work) 4914
    R-Factor(R-Work) 0.1719
    R-Factor(R-Free) 0.2346
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3214
    Shell Resolution(Low) 4.4042
    Number of Reflections(R-Free) 256
    Number of Reflections(R-Work) 4907
    R-Factor(R-Work) 0.1715
    R-Factor(R-Free) 0.2337
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4042
    Shell Resolution(Low) 4.4938
    Number of Reflections(R-Free) 294
    Number of Reflections(R-Work) 4872
    R-Factor(R-Work) 0.1678
    R-Factor(R-Free) 0.2254
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4938
    Shell Resolution(Low) 4.5912
    Number of Reflections(R-Free) 249
    Number of Reflections(R-Work) 4930
    R-Factor(R-Work) 0.1583
    R-Factor(R-Free) 0.2091
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5912
    Shell Resolution(Low) 4.6976
    Number of Reflections(R-Free) 230
    Number of Reflections(R-Work) 4945
    R-Factor(R-Work) 0.1535
    R-Factor(R-Free) 0.1948
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6976
    Shell Resolution(Low) 4.8146
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 4913
    R-Factor(R-Work) 0.1464
    R-Factor(R-Free) 0.2108
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8146
    Shell Resolution(Low) 4.9442
    Number of Reflections(R-Free) 262
    Number of Reflections(R-Work) 4894
    R-Factor(R-Work) 0.1369
    R-Factor(R-Free) 0.2025
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9442
    Shell Resolution(Low) 5.089
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 4905
    R-Factor(R-Work) 0.1416
    R-Factor(R-Free) 0.2058
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.089
    Shell Resolution(Low) 5.2524
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 4938
    R-Factor(R-Work) 0.1352
    R-Factor(R-Free) 0.2083
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2524
    Shell Resolution(Low) 5.439
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 4887
    R-Factor(R-Work) 0.1253
    R-Factor(R-Free) 0.1891
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.439
    Shell Resolution(Low) 5.6554
    Number of Reflections(R-Free) 261
    Number of Reflections(R-Work) 4840
    R-Factor(R-Work) 0.1268
    R-Factor(R-Free) 0.1959
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6554
    Shell Resolution(Low) 5.9109
    Number of Reflections(R-Free) 250
    Number of Reflections(R-Work) 4860
    R-Factor(R-Work) 0.131
    R-Factor(R-Free) 0.1911
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9109
    Shell Resolution(Low) 6.2198
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 4824
    R-Factor(R-Work) 0.142
    R-Factor(R-Free) 0.2267
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2198
    Shell Resolution(Low) 6.6055
    Number of Reflections(R-Free) 251
    Number of Reflections(R-Work) 4869
    R-Factor(R-Work) 0.139
    R-Factor(R-Free) 0.1991
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6055
    Shell Resolution(Low) 7.1091
    Number of Reflections(R-Free) 250
    Number of Reflections(R-Work) 4870
    R-Factor(R-Work) 0.1313
    R-Factor(R-Free) 0.1925
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1091
    Shell Resolution(Low) 7.8128
    Number of Reflections(R-Free) 248
    Number of Reflections(R-Work) 4824
    R-Factor(R-Work) 0.1236
    R-Factor(R-Free) 0.1919
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.8128
    Shell Resolution(Low) 8.9167
    Number of Reflections(R-Free) 259
    Number of Reflections(R-Work) 4778
    R-Factor(R-Work) 0.1345
    R-Factor(R-Free) 0.188
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.9167
    Shell Resolution(Low) 11.1354
    Number of Reflections(R-Free) 249
    Number of Reflections(R-Work) 4783
    R-Factor(R-Work) 0.1459
    R-Factor(R-Free) 0.2006
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 11.1354
    Shell Resolution(Low) 29.7716
    Number of Reflections(R-Free) 254
    Number of Reflections(R-Work) 4586
    R-Factor(R-Work) 0.2123
    R-Factor(R-Free) 0.2462
    Percent Reflections(Observed) 86.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 20.336
    f_plane_restr 0.009
    f_chiral_restr 0.089
    f_angle_d 1.59
    f_bond_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19088
    Nucleic Acid Atoms 32509
    Heterogen Atoms 291
    Solvent Atoms 416
     
     
  •   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