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X-RAY DIFFRACTION
Materials and Methods page
2YNM
  •   Crystallization Hide
    Crystallization Experiments
    pH 7.5
    Details CRYSTALLIZED FROM 3% (W/V) PEG 6000, 100MM KCL, 100MM TRIS, PH 8.5; THEN SOAKED WITH 13% (W/V) PEG 8000, 100MM HEPES, PH 7.5, 15% (V/V) GLYCEROL, 5MM DTT, 0.01MM PCHLIDE, 24MM DMSO
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 308.4 α = 90
    b = 74.11 β = 91.24
    c = 74.23 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX
    Details MIRRORS
    Collection Date 2010-12-17
     
    Diffraction Radiation
    Monochromator SI(111) DOUBLE CRYSTAL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type BESSY BEAMLINE 14.2
    Wavelength 0.91841
    Site BESSY
    Beamline 14.2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 3.0
    Resolution(High) 2.1
    Resolution(Low) 34.51
    Number Reflections(Observed) 81370
    Percent Possible(Observed) 83.1
    R Merge I(Observed) 0.05
    B(Isotropic) From Wilson Plot 23.56
    Redundancy 2.6
     
    High Resolution Shell Details
    Resolution(High) 2.1
    Resolution(Low) 2.18
    Percent Possible(All) 48.2
    R Merge I(Observed) 0.26
    Mean I Over Sigma(Observed) 3.0
    Redundancy 0.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.1
    Resolution(Low) 34.51
    Cut-off Sigma(F) 1.99
    Number of Reflections(Observed) 81361
    Number of Reflections(R-Free) 4028
    Percent Reflections(Observed) 83.09
    R-Factor(Observed) 0.2006
    R-Work 0.1989
    R-Free 0.2331
     
    Temperature Factor Modeling
    Mean Isotropic B Value 41.4
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1
    Shell Resolution(Low) 2.1247
    Number of Reflections(R-Free) 69
    Number of Reflections(R-Work) 1387
    R-Factor(R-Work) 0.2612
    R-Factor(R-Free) 0.3287
    Percent Reflections(Observed) 43.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1247
    Shell Resolution(Low) 2.1506
    Number of Reflections(R-Free) 75
    Number of Reflections(R-Work) 1557
    R-Factor(R-Work) 0.2532
    R-Factor(R-Free) 0.3321
    Percent Reflections(Observed) 49.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1506
    Shell Resolution(Low) 2.1778
    Number of Reflections(R-Free) 93
    Number of Reflections(R-Work) 1697
    R-Factor(R-Work) 0.2358
    R-Factor(R-Free) 0.3069
    Percent Reflections(Observed) 53.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1778
    Shell Resolution(Low) 2.2065
    Number of Reflections(R-Free) 94
    Number of Reflections(R-Work) 1768
    R-Factor(R-Work) 0.2383
    R-Factor(R-Free) 0.2787
    Percent Reflections(Observed) 56.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2065
    Shell Resolution(Low) 2.2367
    Number of Reflections(R-Free) 87
    Number of Reflections(R-Work) 1896
    R-Factor(R-Work) 0.2434
    R-Factor(R-Free) 0.2967
    Percent Reflections(Observed) 59.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2367
    Shell Resolution(Low) 2.2687
    Number of Reflections(R-Free) 98
    Number of Reflections(R-Work) 1955
    R-Factor(R-Work) 0.2367
    R-Factor(R-Free) 0.3049
    Percent Reflections(Observed) 62.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2687
    Shell Resolution(Low) 2.3025
    Number of Reflections(R-Free) 110
    Number of Reflections(R-Work) 2079
    R-Factor(R-Work) 0.2482
    R-Factor(R-Free) 0.3183
    Percent Reflections(Observed) 65.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3025
    Shell Resolution(Low) 2.3385
    Number of Reflections(R-Free) 103
    Number of Reflections(R-Work) 2179
    R-Factor(R-Work) 0.2624
    R-Factor(R-Free) 0.3203
    Percent Reflections(Observed) 68.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3385
    Shell Resolution(Low) 2.3768
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2265
    R-Factor(R-Work) 0.2601
    R-Factor(R-Free) 0.2544
    Percent Reflections(Observed) 71.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3768
    Shell Resolution(Low) 2.4178
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 2381
    R-Factor(R-Work) 0.2481
    R-Factor(R-Free) 0.2893
    Percent Reflections(Observed) 75.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4178
    Shell Resolution(Low) 2.4617
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2498
    R-Factor(R-Work) 0.2555
    R-Factor(R-Free) 0.2923
    Percent Reflections(Observed) 78.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4617
    Shell Resolution(Low) 2.5091
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.2498
    R-Factor(R-Free) 0.3315
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5091
    Shell Resolution(Low) 2.5603
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2791
    R-Factor(R-Work) 0.2514
    R-Factor(R-Free) 0.2918
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5603
    Shell Resolution(Low) 2.6159
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2807
    R-Factor(R-Work) 0.2537
    R-Factor(R-Free) 0.2993
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6159
    Shell Resolution(Low) 2.6768
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 3026
    R-Factor(R-Work) 0.251
    R-Factor(R-Free) 0.2995
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6768
    Shell Resolution(Low) 2.7437
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 3163
    R-Factor(R-Work) 0.2547
    R-Factor(R-Free) 0.266
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7437
    Shell Resolution(Low) 2.8178
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 3115
    R-Factor(R-Work) 0.2467
    R-Factor(R-Free) 0.297
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8178
    Shell Resolution(Low) 2.9007
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 3157
    R-Factor(R-Work) 0.2413
    R-Factor(R-Free) 0.2885
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9007
    Shell Resolution(Low) 2.9943
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 3155
    R-Factor(R-Work) 0.2228
    R-Factor(R-Free) 0.2902
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9943
    Shell Resolution(Low) 3.1012
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 3154
    R-Factor(R-Work) 0.2269
    R-Factor(R-Free) 0.243
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1012
    Shell Resolution(Low) 3.2253
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 3169
    R-Factor(R-Work) 0.2175
    R-Factor(R-Free) 0.2489
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2253
    Shell Resolution(Low) 3.372
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 3182
    R-Factor(R-Work) 0.2039
    R-Factor(R-Free) 0.2476
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.372
    Shell Resolution(Low) 3.5496
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 3129
    R-Factor(R-Work) 0.188
    R-Factor(R-Free) 0.2272
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5496
    Shell Resolution(Low) 3.7717
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 3177
    R-Factor(R-Work) 0.1721
    R-Factor(R-Free) 0.2031
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7717
    Shell Resolution(Low) 4.0625
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 3167
    R-Factor(R-Work) 0.1602
    R-Factor(R-Free) 0.1948
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0625
    Shell Resolution(Low) 4.4706
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 3170
    R-Factor(R-Work) 0.1442
    R-Factor(R-Free) 0.1743
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4706
    Shell Resolution(Low) 5.1157
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 3203
    R-Factor(R-Work) 0.14
    R-Factor(R-Free) 0.1593
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1157
    Shell Resolution(Low) 6.4384
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3212
    R-Factor(R-Work) 0.1642
    R-Factor(R-Free) 0.209
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.4384
    Shell Resolution(Low) 34.5148
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3278
    R-Factor(R-Work) 0.1512
    R-Factor(R-Free) 0.1502
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.003
    f_chiral_restr 0.053
    f_dihedral_angle_d 13.458
    f_angle_d 1.018
    f_bond_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 11195
    Nucleic Acid Atoms 0
    Heterogen Atoms 226
    Solvent Atoms 382
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHENIX.AUTO_MR
    Structure Refinement PHENIX (PHENIX.REFINE: 1.8.1_1168)
     
    Software
    refinement PHENIX version: (PHENIX.REFINE: 1.8.1_1168)
    model building PHENIX.AUTO_MR