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X-RAY DIFFRACTION
Materials and Methods page
4DV5
  •   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 = 402.13 α = 90
    b = 402.13 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 2010-11-07
     
    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) 3.68
    Resolution(Low) 35
    Number Reflections(All) 149012
    Number Reflections(Observed) 149012
    Percent Possible(Observed) 98.3
    R Merge I(Observed) 0.102
    Redundancy 2.9
     
    High Resolution Shell Details
    Resolution(High) 3.683
    Resolution(Low) 3.83
    Percent Possible(All) 98.5
    R Merge I(Observed) 0.608
    Redundancy 2.7
    Number Unique Reflections(All) 14757
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.683
    Resolution(Low) 34.555
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 148962
    Number of Reflections(Observed) 148962
    Number of Reflections(R-Free) 7392
    Percent Reflections(Observed) 98.14
    R-Factor(Observed) 0.1586
    R-Work 0.1558
    R-Free 0.2115
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 148.635
    Anisotropic B[1][1] -14.4644
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -14.4644
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 22.2271
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.683
    Shell Resolution(Low) 3.7249
    Number of Reflections(R-Free) 224
    Number of Reflections(R-Work) 4453
    R-Factor(R-Work) 0.2741
    R-Factor(R-Free) 0.3282
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7249
    Shell Resolution(Low) 3.7686
    Number of Reflections(R-Free) 272
    Number of Reflections(R-Work) 4678
    R-Factor(R-Work) 0.248
    R-Factor(R-Free) 0.3026
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7686
    Shell Resolution(Low) 3.8145
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 4727
    R-Factor(R-Work) 0.2449
    R-Factor(R-Free) 0.3277
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8145
    Shell Resolution(Low) 3.8628
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 4708
    R-Factor(R-Work) 0.2302
    R-Factor(R-Free) 0.289
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8628
    Shell Resolution(Low) 3.9135
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 4757
    R-Factor(R-Work) 0.2227
    R-Factor(R-Free) 0.2696
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9135
    Shell Resolution(Low) 3.9671
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 4723
    R-Factor(R-Work) 0.2129
    R-Factor(R-Free) 0.259
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9671
    Shell Resolution(Low) 4.0237
    Number of Reflections(R-Free) 273
    Number of Reflections(R-Work) 4740
    R-Factor(R-Work) 0.2168
    R-Factor(R-Free) 0.281
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0237
    Shell Resolution(Low) 4.0836
    Number of Reflections(R-Free) 274
    Number of Reflections(R-Work) 4705
    R-Factor(R-Work) 0.2029
    R-Factor(R-Free) 0.2583
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0836
    Shell Resolution(Low) 4.1473
    Number of Reflections(R-Free) 240
    Number of Reflections(R-Work) 4738
    R-Factor(R-Work) 0.1835
    R-Factor(R-Free) 0.2352
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1473
    Shell Resolution(Low) 4.2152
    Number of Reflections(R-Free) 245
    Number of Reflections(R-Work) 4771
    R-Factor(R-Work) 0.1728
    R-Factor(R-Free) 0.262
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2152
    Shell Resolution(Low) 4.2878
    Number of Reflections(R-Free) 240
    Number of Reflections(R-Work) 4739
    R-Factor(R-Work) 0.173
    R-Factor(R-Free) 0.2262
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2878
    Shell Resolution(Low) 4.3656
    Number of Reflections(R-Free) 267
    Number of Reflections(R-Work) 4718
    R-Factor(R-Work) 0.1676
    R-Factor(R-Free) 0.2386
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3656
    Shell Resolution(Low) 4.4494
    Number of Reflections(R-Free) 267
    Number of Reflections(R-Work) 4731
    R-Factor(R-Work) 0.1603
    R-Factor(R-Free) 0.2137
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4494
    Shell Resolution(Low) 4.54
    Number of Reflections(R-Free) 262
    Number of Reflections(R-Work) 4731
    R-Factor(R-Work) 0.1538
    R-Factor(R-Free) 0.2224
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.54
    Shell Resolution(Low) 4.6385
    Number of Reflections(R-Free) 235
    Number of Reflections(R-Work) 4743
    R-Factor(R-Work) 0.1446
    R-Factor(R-Free) 0.1915
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6385
    Shell Resolution(Low) 4.7461
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 4767
    R-Factor(R-Work) 0.1397
    R-Factor(R-Free) 0.2195
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7461
    Shell Resolution(Low) 4.8645
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 4781
    R-Factor(R-Work) 0.1366
    R-Factor(R-Free) 0.1958
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8645
    Shell Resolution(Low) 4.9957
    Number of Reflections(R-Free) 264
    Number of Reflections(R-Work) 4714
    R-Factor(R-Work) 0.1314
    R-Factor(R-Free) 0.2018
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9957
    Shell Resolution(Low) 5.1422
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 4781
    R-Factor(R-Work) 0.1295
    R-Factor(R-Free) 0.2099
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1422
    Shell Resolution(Low) 5.3076
    Number of Reflections(R-Free) 246
    Number of Reflections(R-Work) 4723
    R-Factor(R-Work) 0.1268
    R-Factor(R-Free) 0.1976
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3076
    Shell Resolution(Low) 5.4966
    Number of Reflections(R-Free) 253
    Number of Reflections(R-Work) 4752
    R-Factor(R-Work) 0.1183
    R-Factor(R-Free) 0.1752
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4966
    Shell Resolution(Low) 5.7157
    Number of Reflections(R-Free) 247
    Number of Reflections(R-Work) 4731
    R-Factor(R-Work) 0.1178
    R-Factor(R-Free) 0.2038
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7157
    Shell Resolution(Low) 5.9746
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 4753
    R-Factor(R-Work) 0.1237
    R-Factor(R-Free) 0.1659
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9746
    Shell Resolution(Low) 6.2878
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 4738
    R-Factor(R-Work) 0.1217
    R-Factor(R-Free) 0.1892
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2878
    Shell Resolution(Low) 6.6791
    Number of Reflections(R-Free) 251
    Number of Reflections(R-Work) 4735
    R-Factor(R-Work) 0.1194
    R-Factor(R-Free) 0.1733
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6791
    Shell Resolution(Low) 7.1905
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 4721
    R-Factor(R-Work) 0.1162
    R-Factor(R-Free) 0.1703
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.1905
    Shell Resolution(Low) 7.9063
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 4697
    R-Factor(R-Work) 0.1164
    R-Factor(R-Free) 0.1818
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.9063
    Shell Resolution(Low) 9.0325
    Number of Reflections(R-Free) 270
    Number of Reflections(R-Work) 4633
    R-Factor(R-Work) 0.1195
    R-Factor(R-Free) 0.1588
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.0325
    Shell Resolution(Low) 11.3133
    Number of Reflections(R-Free) 239
    Number of Reflections(R-Work) 4740
    R-Factor(R-Work) 0.1352
    R-Factor(R-Free) 0.1792
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 11.3133
    Shell Resolution(Low) 34.5564
    Number of Reflections(R-Free) 258
    Number of Reflections(R-Work) 4642
    R-Factor(R-Work) 0.2114
    R-Factor(R-Free) 0.237
    Percent Reflections(Observed) 90.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 20.674
    f_plane_restr 0.01
    f_chiral_restr 0.099
    f_angle_d 1.821
    f_bond_d 0.015
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19088
    Nucleic Acid Atoms 32508
    Heterogen Atoms 315
    Solvent Atoms 389
     
     
  •   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