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X-RAY DIFFRACTION
Materials and Methods page
4MGN
  •   Crystallization Hide
    Crystallization Experiments
    Method hanging drop
    pH 7
    Temperature 291.0
    Details 80mM NaCl, 20mM MgCl2, 40mM sodium cacodylate, 12mM spermine, 10% 2-methyl-1,3 propanediol, pH 7.0, hanging drop, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 92.84 α = 90
    b = 205.18 β = 90
    c = 161.42 γ = 90
     
    Space Group
    Space Group Name:    C 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2013-03-07
     
    Diffraction Radiation
    Monochromator Cryogenically-cooled single crystal Si(220) side bounce monochromator.
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-E
    Wavelength List 0.979
    Site APS
    Beamline 24-ID-E
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 3.2
    Resolution(Low) 50
    Number Reflections(Observed) 26207
    Percent Possible(Observed) 98.8
    R Merge I(Observed) 0.16
    B(Isotropic) From Wilson Plot 74.54
    Redundancy 6.9
     
    High Resolution Shell Details
    Resolution(High) 3.2
    Resolution(Low) 3.26
    Percent Possible(All) 96.9
    Mean I Over Sigma(Observed) 2.29
    Redundancy 6.1
    Number Unique Reflections(All) 1289
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.2
    Resolution(Low) 43.292
    Cut-off Sigma(F) 1.33
    Number of Reflections(Observed) 25268
    Number of Reflections(R-Free) 2512
    Percent Reflections(Observed) 97.85
    R-Factor(Observed) 0.2406
    R-Work 0.2364
    R-Free 0.2783
     
    Temperature Factor Modeling
    Mean Isotropic B Value 141.604
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2001
    Shell Resolution(Low) 3.2616
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 1176
    R-Factor(R-Work) 0.342
    R-Factor(R-Free) 0.3608
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2616
    Shell Resolution(Low) 3.3281
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1213
    R-Factor(R-Work) 0.3402
    R-Factor(R-Free) 0.3719
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3281
    Shell Resolution(Low) 3.4005
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1205
    R-Factor(R-Work) 0.3413
    R-Factor(R-Free) 0.3437
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4005
    Shell Resolution(Low) 3.4796
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1195
    R-Factor(R-Work) 0.3347
    R-Factor(R-Free) 0.3443
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4796
    Shell Resolution(Low) 3.5665
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1243
    R-Factor(R-Work) 0.3313
    R-Factor(R-Free) 0.3621
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5665
    Shell Resolution(Low) 3.6629
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 1244
    R-Factor(R-Work) 0.321
    R-Factor(R-Free) 0.3602
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6629
    Shell Resolution(Low) 3.7706
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1250
    R-Factor(R-Work) 0.3057
    R-Factor(R-Free) 0.3581
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7706
    Shell Resolution(Low) 3.8923
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1264
    R-Factor(R-Work) 0.2659
    R-Factor(R-Free) 0.325
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8923
    Shell Resolution(Low) 4.0313
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 1268
    R-Factor(R-Work) 0.2664
    R-Factor(R-Free) 0.3028
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0313
    Shell Resolution(Low) 4.1926
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 1258
    R-Factor(R-Work) 0.275
    R-Factor(R-Free) 0.3382
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1926
    Shell Resolution(Low) 4.3832
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1283
    R-Factor(R-Work) 0.2687
    R-Factor(R-Free) 0.3519
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3832
    Shell Resolution(Low) 4.614
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1276
    R-Factor(R-Work) 0.2573
    R-Factor(R-Free) 0.3099
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.614
    Shell Resolution(Low) 4.9028
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 1289
    R-Factor(R-Work) 0.248
    R-Factor(R-Free) 0.2822
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9028
    Shell Resolution(Low) 5.2807
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1281
    R-Factor(R-Work) 0.2144
    R-Factor(R-Free) 0.2321
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2807
    Shell Resolution(Low) 5.811
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1313
    R-Factor(R-Work) 0.2025
    R-Factor(R-Free) 0.2744
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.811
    Shell Resolution(Low) 6.6492
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1317
    R-Factor(R-Work) 0.2229
    R-Factor(R-Free) 0.2494
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6492
    Shell Resolution(Low) 8.3674
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1321
    R-Factor(R-Work) 0.2085
    R-Factor(R-Free) 0.2291
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.3674
    Shell Resolution(Low) 43.2959
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 1360
    R-Factor(R-Work) 0.1706
    R-Factor(R-Free) 0.2178
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 11.951
    f_plane_restr 0.002
    f_chiral_restr 0.019
    f_angle_d 0.458
    f_bond_d 0.001
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 0
    Nucleic Acid Atoms 6832
    Heterogen Atoms 18
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8.2_1309)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALEPACK