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X-RAY DIFFRACTION
Materials and Methods page
4I4T
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.7
    Temperature 293.0
    Details 3% PEG 4000, 4-6% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 100 mM MES/Imidazole, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 104.77 α = 90
    b = 158.64 β = 90
    c = 179.24 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 PIXEL
    Type PSI PILATUS 6M
    Collection Date 2012-01-29
     
    Diffraction Radiation
    Monochromator LN2 cooled fixed-exit Si(111) monochromator, Sagittally - horizontally focussed
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SLS BEAMLINE X06SA
    Wavelength List 0.99995
    Site SLS
    Beamline X06SA
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.8
    Resolution(Low) 79.4
    Number Reflections(All) 275149
    Number Reflections(Observed) 274535
    R Merge I(Observed) 0.103
    B(Isotropic) From Wilson Plot 33.12
    Redundancy 13.5
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.85
    Percent Possible(All) 99.0
    Mean I Over Sigma(Observed) 1.0
    Redundancy 13.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 79.32
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 274535
    Number of Reflections(Observed) 274515
    Number of Reflections(R-Free) 13945
    Percent Reflections(Observed) 99.77
    R-Factor(Observed) 0.1728
    R-Work 0.1711
    R-Free 0.2043
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 3.1254
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.3509
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -2.1148
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.8205
    Number of Reflections(R-Free) 473
    Number of Reflections(R-Work) 8477
    R-Factor(R-Work) 0.3368
    R-Factor(R-Free) 0.3455
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8205
    Shell Resolution(Low) 1.8419
    Number of Reflections(R-Free) 470
    Number of Reflections(R-Work) 8551
    R-Factor(R-Work) 0.3221
    R-Factor(R-Free) 0.3327
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8419
    Shell Resolution(Low) 1.8643
    Number of Reflections(R-Free) 491
    Number of Reflections(R-Work) 8599
    R-Factor(R-Work) 0.3202
    R-Factor(R-Free) 0.3468
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8643
    Shell Resolution(Low) 1.8879
    Number of Reflections(R-Free) 447
    Number of Reflections(R-Work) 8600
    R-Factor(R-Work) 0.3188
    R-Factor(R-Free) 0.341
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8879
    Shell Resolution(Low) 1.9128
    Number of Reflections(R-Free) 416
    Number of Reflections(R-Work) 8591
    R-Factor(R-Work) 0.2997
    R-Factor(R-Free) 0.3396
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9128
    Shell Resolution(Low) 1.939
    Number of Reflections(R-Free) 490
    Number of Reflections(R-Work) 8594
    R-Factor(R-Work) 0.2954
    R-Factor(R-Free) 0.327
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.939
    Shell Resolution(Low) 1.9667
    Number of Reflections(R-Free) 499
    Number of Reflections(R-Work) 8553
    R-Factor(R-Work) 0.2752
    R-Factor(R-Free) 0.303
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9667
    Shell Resolution(Low) 1.9961
    Number of Reflections(R-Free) 478
    Number of Reflections(R-Work) 8600
    R-Factor(R-Work) 0.251
    R-Factor(R-Free) 0.2642
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9961
    Shell Resolution(Low) 2.0272
    Number of Reflections(R-Free) 448
    Number of Reflections(R-Work) 8642
    R-Factor(R-Work) 0.2349
    R-Factor(R-Free) 0.2611
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0272
    Shell Resolution(Low) 2.0605
    Number of Reflections(R-Free) 502
    Number of Reflections(R-Work) 8582
    R-Factor(R-Work) 0.229
    R-Factor(R-Free) 0.2757
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0605
    Shell Resolution(Low) 2.096
    Number of Reflections(R-Free) 448
    Number of Reflections(R-Work) 8621
    R-Factor(R-Work) 0.2167
    R-Factor(R-Free) 0.2501
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.096
    Shell Resolution(Low) 2.1341
    Number of Reflections(R-Free) 476
    Number of Reflections(R-Work) 8633
    R-Factor(R-Work) 0.1984
    R-Factor(R-Free) 0.2351
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1341
    Shell Resolution(Low) 2.1752
    Number of Reflections(R-Free) 437
    Number of Reflections(R-Work) 8654
    R-Factor(R-Work) 0.1808
    R-Factor(R-Free) 0.2213
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1752
    Shell Resolution(Low) 2.2196
    Number of Reflections(R-Free) 462
    Number of Reflections(R-Work) 8633
    R-Factor(R-Work) 0.1757
    R-Factor(R-Free) 0.2162
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2196
    Shell Resolution(Low) 2.2679
    Number of Reflections(R-Free) 443
    Number of Reflections(R-Work) 8706
    R-Factor(R-Work) 0.1777
    R-Factor(R-Free) 0.2113
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2679
    Shell Resolution(Low) 2.3206
    Number of Reflections(R-Free) 483
    Number of Reflections(R-Work) 8632
    R-Factor(R-Work) 0.1669
    R-Factor(R-Free) 0.2152
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3206
    Shell Resolution(Low) 2.3786
    Number of Reflections(R-Free) 447
    Number of Reflections(R-Work) 8692
    R-Factor(R-Work) 0.1629
    R-Factor(R-Free) 0.2017
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3786
    Shell Resolution(Low) 2.443
    Number of Reflections(R-Free) 488
    Number of Reflections(R-Work) 8668
    R-Factor(R-Work) 0.1541
    R-Factor(R-Free) 0.1898
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.443
    Shell Resolution(Low) 2.5149
    Number of Reflections(R-Free) 444
    Number of Reflections(R-Work) 8668
    R-Factor(R-Work) 0.151
    R-Factor(R-Free) 0.2032
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5149
    Shell Resolution(Low) 2.596
    Number of Reflections(R-Free) 471
    Number of Reflections(R-Work) 8694
    R-Factor(R-Work) 0.1626
    R-Factor(R-Free) 0.2036
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.596
    Shell Resolution(Low) 2.6888
    Number of Reflections(R-Free) 448
    Number of Reflections(R-Work) 8736
    R-Factor(R-Work) 0.1648
    R-Factor(R-Free) 0.2066
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6888
    Shell Resolution(Low) 2.7965
    Number of Reflections(R-Free) 485
    Number of Reflections(R-Work) 8662
    R-Factor(R-Work) 0.1669
    R-Factor(R-Free) 0.217
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7965
    Shell Resolution(Low) 2.9238
    Number of Reflections(R-Free) 436
    Number of Reflections(R-Work) 8761
    R-Factor(R-Work) 0.1617
    R-Factor(R-Free) 0.2083
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9238
    Shell Resolution(Low) 3.0779
    Number of Reflections(R-Free) 438
    Number of Reflections(R-Work) 8753
    R-Factor(R-Work) 0.16
    R-Factor(R-Free) 0.1838
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0779
    Shell Resolution(Low) 3.2708
    Number of Reflections(R-Free) 436
    Number of Reflections(R-Work) 8789
    R-Factor(R-Work) 0.1686
    R-Factor(R-Free) 0.2041
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2708
    Shell Resolution(Low) 3.5233
    Number of Reflections(R-Free) 498
    Number of Reflections(R-Work) 8759
    R-Factor(R-Work) 0.1701
    R-Factor(R-Free) 0.2076
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5233
    Shell Resolution(Low) 3.8778
    Number of Reflections(R-Free) 463
    Number of Reflections(R-Work) 8798
    R-Factor(R-Work) 0.1544
    R-Factor(R-Free) 0.1852
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8778
    Shell Resolution(Low) 4.4389
    Number of Reflections(R-Free) 446
    Number of Reflections(R-Work) 8840
    R-Factor(R-Work) 0.1265
    R-Factor(R-Free) 0.1541
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4389
    Shell Resolution(Low) 5.5924
    Number of Reflections(R-Free) 491
    Number of Reflections(R-Work) 8903
    R-Factor(R-Work) 0.1283
    R-Factor(R-Free) 0.1506
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5924
    Shell Resolution(Low) 79.3971
    Number of Reflections(R-Free) 491
    Number of Reflections(R-Work) 9179
    R-Factor(R-Work) 0.1868
    R-Factor(R-Free) 0.2139
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.069
    f_dihedral_angle_d 14.703
    f_angle_d 1.179
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 17547
    Nucleic Acid Atoms 0
    Heterogen Atoms 265
    Solvent Atoms 1522
     
     
  •   Software and Computing Hide
    Computing
    Data Collection REMDAQ
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.3_928)
    model building PHASER
    data collection REMDAQ