POP-OUT | CLOSE

An Information Portal to 106082 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4FYD
  •   Crystallization Hide
    Crystallization Experiments
    Method microbatch
    Temperature 291.0
    Details 0.2M MgAc2, 10% PEG8000, microbatch, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 111.69 α = 90
    b = 145.69 β = 90
    c = 197.2 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2011-01-01
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I02
    Wavelength List 0.9795
    Site DIAMOND
    Beamline I02
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 3.1
    Resolution(Low) 49.39
    Number Reflections(All) 59154
    Number Reflections(Observed) 59154
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.105
    B(Isotropic) From Wilson Plot 97.34
    Redundancy 7.2
     
    High Resolution Shell Details
    Resolution(High) 3.1
    Resolution(Low) 3.26
    Percent Possible(All) 98.4
    R Merge I(Observed) 0.974
    Mean I Over Sigma(Observed) 2.1
    R-Sym I(Observed) 0.974
    Redundancy 7.3
    Number Unique Reflections(All) 8380
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.1
    Resolution(Low) 48.801
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 59154
    Number of Reflections(Observed) 59154
    Number of Reflections(R-Free) 5699
    Percent Reflections(Observed) 99.21
    R-Factor(Observed) 0.2116
    R-Work 0.2098
    R-Free 0.2467
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1
    Shell Resolution(Low) 3.1322
    Number of Reflections(R-Free) 199
    Number of Reflections(R-Work) 3358
    R-Factor(R-Work) 0.3849
    R-Factor(R-Free) 0.4081
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1322
    Shell Resolution(Low) 3.169
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 3561
    R-Factor(R-Work) 0.3588
    R-Factor(R-Free) 0.4015
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.169
    Shell Resolution(Low) 3.2077
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 3576
    R-Factor(R-Work) 0.3335
    R-Factor(R-Free) 0.371
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2077
    Shell Resolution(Low) 3.2483
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 3504
    R-Factor(R-Work) 0.325
    R-Factor(R-Free) 0.3472
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2483
    Shell Resolution(Low) 3.291
    Number of Reflections(R-Free) 196
    Number of Reflections(R-Work) 3587
    R-Factor(R-Work) 0.3047
    R-Factor(R-Free) 0.3074
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.291
    Shell Resolution(Low) 3.3361
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 3519
    R-Factor(R-Work) 0.2919
    R-Factor(R-Free) 0.3305
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3361
    Shell Resolution(Low) 3.3837
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3635
    R-Factor(R-Work) 0.2736
    R-Factor(R-Free) 0.3373
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3837
    Shell Resolution(Low) 3.4342
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 3491
    R-Factor(R-Work) 0.2776
    R-Factor(R-Free) 0.3237
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4342
    Shell Resolution(Low) 3.4879
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3604
    R-Factor(R-Work) 0.2638
    R-Factor(R-Free) 0.2796
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4879
    Shell Resolution(Low) 3.545
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 3556
    R-Factor(R-Work) 0.2508
    R-Factor(R-Free) 0.3466
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.545
    Shell Resolution(Low) 3.6061
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 3571
    R-Factor(R-Work) 0.2493
    R-Factor(R-Free) 0.2915
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6061
    Shell Resolution(Low) 3.6717
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 3502
    R-Factor(R-Work) 0.228
    R-Factor(R-Free) 0.2694
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6717
    Shell Resolution(Low) 3.7423
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 3565
    R-Factor(R-Work) 0.232
    R-Factor(R-Free) 0.2565
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7423
    Shell Resolution(Low) 3.8187
    Number of Reflections(R-Free) 200
    Number of Reflections(R-Work) 3534
    R-Factor(R-Work) 0.2392
    R-Factor(R-Free) 0.3009
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8187
    Shell Resolution(Low) 3.9017
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 3602
    R-Factor(R-Work) 0.2233
    R-Factor(R-Free) 0.3517
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9017
    Shell Resolution(Low) 3.9924
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3553
    R-Factor(R-Work) 0.2122
    R-Factor(R-Free) 0.2605
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9924
    Shell Resolution(Low) 4.0922
    Number of Reflections(R-Free) 191
    Number of Reflections(R-Work) 3586
    R-Factor(R-Work) 0.2066
    R-Factor(R-Free) 0.255
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0922
    Shell Resolution(Low) 4.2028
    Number of Reflections(R-Free) 204
    Number of Reflections(R-Work) 3539
    R-Factor(R-Work) 0.1975
    R-Factor(R-Free) 0.2469
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2028
    Shell Resolution(Low) 4.3263
    Number of Reflections(R-Free) 196
    Number of Reflections(R-Work) 3514
    R-Factor(R-Work) 0.1884
    R-Factor(R-Free) 0.265
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3263
    Shell Resolution(Low) 4.4659
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 3564
    R-Factor(R-Work) 0.1829
    R-Factor(R-Free) 0.2055
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4659
    Shell Resolution(Low) 4.6254
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3575
    R-Factor(R-Work) 0.1744
    R-Factor(R-Free) 0.2339
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6254
    Shell Resolution(Low) 4.8104
    Number of Reflections(R-Free) 199
    Number of Reflections(R-Work) 3565
    R-Factor(R-Work) 0.1692
    R-Factor(R-Free) 0.1955
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8104
    Shell Resolution(Low) 5.0292
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3571
    R-Factor(R-Work) 0.1753
    R-Factor(R-Free) 0.2069
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0292
    Shell Resolution(Low) 5.294
    Number of Reflections(R-Free) 201
    Number of Reflections(R-Work) 3534
    R-Factor(R-Work) 0.1932
    R-Factor(R-Free) 0.2167
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.294
    Shell Resolution(Low) 5.6252
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3604
    R-Factor(R-Work) 0.1896
    R-Factor(R-Free) 0.2101
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6252
    Shell Resolution(Low) 6.0588
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 3546
    R-Factor(R-Work) 0.2068
    R-Factor(R-Free) 0.2644
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0588
    Shell Resolution(Low) 6.6672
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3563
    R-Factor(R-Work) 0.2096
    R-Factor(R-Free) 0.2567
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6672
    Shell Resolution(Low) 7.6288
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 3586
    R-Factor(R-Work) 0.2047
    R-Factor(R-Free) 0.2001
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.6288
    Shell Resolution(Low) 9.5995
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3497
    R-Factor(R-Work) 0.1735
    R-Factor(R-Free) 0.2243
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.5995
    Shell Resolution(Low) 48.8069
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 3496
    R-Factor(R-Work) 0.1894
    R-Factor(R-Free) 0.178
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.039
    f_dihedral_angle_d 15.43
    f_angle_d 0.652
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 13530
    Nucleic Acid Atoms 1152
    Heterogen Atoms 62
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: dev_1078)
     
    Software
    refinement PHENIX version: (phenix.refine: dev_1078)
    model building PHASER
    data collection ADSC version: Quantum