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X-RAY DIFFRACTION
Materials and Methods page
2YME
  •   Crystallization Hide
    Crystallization Experiments
    Details 200 MM NA2SO4, BISTRISPROPANE PH 8.5, 18% PEG3350.
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 83.09 α = 90
    b = 138.9 β = 91.07
    c = 119.89 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC
    Collection Date 2009-06-12
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID23-1
    Wavelength 0.87260
    Site ESRF
    Beamline ID23-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 1.5
    Resolution(High) 2.4
    Resolution(Low) 46.35
    Number Reflections(Observed) 105875
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.12
    B(Isotropic) From Wilson Plot 35.58
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 2.4
    Resolution(Low) 2.5
    Percent Possible(All) 99.9
    R Merge I(Observed) 0.8
    Mean I Over Sigma(Observed) 1.5
    Redundancy 3.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.4
    Resolution(Low) 48.908
    Cut-off Sigma(F) 1.99
    Number of Reflections(Observed) 105852
    Number of Reflections(R-Free) 5292
    Percent Reflections(Observed) 99.71
    R-Factor(Observed) 0.1724
    R-Work 0.1695
    R-Free 0.2263
     
    Temperature Factor Modeling
    Mean Isotropic B Value 46.0
    Anisotropic B[1][1] 0.9392
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -7.0484
    Anisotropic B[2][2] -6.3015
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 5.3623
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3999
    Shell Resolution(Low) 2.4272
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3308
    R-Factor(R-Work) 0.2898
    R-Factor(R-Free) 0.3448
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4272
    Shell Resolution(Low) 2.4557
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3390
    R-Factor(R-Work) 0.2754
    R-Factor(R-Free) 0.3544
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4557
    Shell Resolution(Low) 2.4857
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3349
    R-Factor(R-Work) 0.263
    R-Factor(R-Free) 0.3174
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4857
    Shell Resolution(Low) 2.5172
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 3354
    R-Factor(R-Work) 0.263
    R-Factor(R-Free) 0.3391
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5172
    Shell Resolution(Low) 2.5503
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 3331
    R-Factor(R-Work) 0.2537
    R-Factor(R-Free) 0.3248
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5503
    Shell Resolution(Low) 2.5852
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3349
    R-Factor(R-Work) 0.2466
    R-Factor(R-Free) 0.3058
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5852
    Shell Resolution(Low) 2.6221
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 3339
    R-Factor(R-Work) 0.2365
    R-Factor(R-Free) 0.318
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6221
    Shell Resolution(Low) 2.6613
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 3362
    R-Factor(R-Work) 0.2308
    R-Factor(R-Free) 0.3111
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6613
    Shell Resolution(Low) 2.7029
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 3316
    R-Factor(R-Work) 0.2208
    R-Factor(R-Free) 0.3037
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7029
    Shell Resolution(Low) 2.7472
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3361
    R-Factor(R-Work) 0.23
    R-Factor(R-Free) 0.2898
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7472
    Shell Resolution(Low) 2.7945
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3355
    R-Factor(R-Work) 0.2064
    R-Factor(R-Free) 0.2986
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7945
    Shell Resolution(Low) 2.8453
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 3335
    R-Factor(R-Work) 0.1997
    R-Factor(R-Free) 0.2722
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8453
    Shell Resolution(Low) 2.9001
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 3346
    R-Factor(R-Work) 0.1979
    R-Factor(R-Free) 0.2911
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9001
    Shell Resolution(Low) 2.9593
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3389
    R-Factor(R-Work) 0.19
    R-Factor(R-Free) 0.2739
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9593
    Shell Resolution(Low) 3.0236
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 3311
    R-Factor(R-Work) 0.1907
    R-Factor(R-Free) 0.2403
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0236
    Shell Resolution(Low) 3.0939
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 3357
    R-Factor(R-Work) 0.1716
    R-Factor(R-Free) 0.2671
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0939
    Shell Resolution(Low) 3.1713
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3364
    R-Factor(R-Work) 0.1713
    R-Factor(R-Free) 0.2447
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1713
    Shell Resolution(Low) 3.257
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 3310
    R-Factor(R-Work) 0.1716
    R-Factor(R-Free) 0.2216
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.257
    Shell Resolution(Low) 3.3528
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3372
    R-Factor(R-Work) 0.1646
    R-Factor(R-Free) 0.2316
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3528
    Shell Resolution(Low) 3.461
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3387
    R-Factor(R-Work) 0.1622
    R-Factor(R-Free) 0.222
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.461
    Shell Resolution(Low) 3.5847
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 3314
    R-Factor(R-Work) 0.1597
    R-Factor(R-Free) 0.2273
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5847
    Shell Resolution(Low) 3.7282
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 3353
    R-Factor(R-Work) 0.1515
    R-Factor(R-Free) 0.2025
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7282
    Shell Resolution(Low) 3.8978
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3362
    R-Factor(R-Work) 0.1412
    R-Factor(R-Free) 0.187
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8978
    Shell Resolution(Low) 4.1032
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3362
    R-Factor(R-Work) 0.1334
    R-Factor(R-Free) 0.181
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1032
    Shell Resolution(Low) 4.3601
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 3343
    R-Factor(R-Work) 0.123
    R-Factor(R-Free) 0.1807
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3601
    Shell Resolution(Low) 4.6965
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 3340
    R-Factor(R-Work) 0.1149
    R-Factor(R-Free) 0.1686
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6965
    Shell Resolution(Low) 5.1686
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3373
    R-Factor(R-Work) 0.1107
    R-Factor(R-Free) 0.1523
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1686
    Shell Resolution(Low) 5.9155
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3368
    R-Factor(R-Work) 0.1442
    R-Factor(R-Free) 0.1995
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9155
    Shell Resolution(Low) 7.4486
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3373
    R-Factor(R-Work) 0.1631
    R-Factor(R-Free) 0.2071
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.4486
    Shell Resolution(Low) 48.9184
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3387
    R-Factor(R-Work) 0.1758
    R-Factor(R-Free) 0.1963
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.051
    f_dihedral_angle_d 20.142
    f_angle_d 0.805
    f_bond_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 16400
    Nucleic Acid Atoms 0
    Heterogen Atoms 382
    Solvent Atoms 1251
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution MOLREP
    Structure Refinement PHENIX (PHENIX.REFINE)
     
    Software
    refinement PHENIX version: (PHENIX.REFINE)
    model building MOLREP