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X-RAY DIFFRACTION
Materials and Methods page
4INM
  •   Crystallization Hide
    Crystallization Experiments
    pH 7.5
    Temperature 294.0
    Details 10% MPD, 40mM sodium cacodylate, 24mM spermine tetra-HCL, 80mM sodium chloride, 20mM magnesium chloride, 35% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 102.99 α = 90
    b = 176.1 β = 90
    c = 208.85 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 274
    Diffrn ID 2
    Data Collection Temperature 274
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-06-22
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-08-13
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength 1.075
    Site NSLS
    Beamline X29A
    Source SYNCHROTRON
    Type APS BEAMLINE 23-ID-D
    Wavelength 1.033
    Site APS
    Beamline 23-ID-D
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.5
    Resolution(Low) 50
    Number Reflections(Observed) 46684
    Percent Possible(Observed) 96.1
    R Merge I(Observed) 0.118
    Redundancy 4.0
     
    High Resolution Shell Details
    Resolution(High) 3.5
    Resolution(Low) 3.56
    Percent Possible(All) 78.7
    R Merge I(Observed) 0.695
    Mean I Over Sigma(Observed) 1.5
    Redundancy 3.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.5
    Resolution(Low) 49.54
    Number of Reflections(all) 88375
    Number of Reflections(Observed) 46684
    Number of Reflections(R-Free) 3364
    Percent Reflections(Observed) 95.55
    R-Work 0.235
    R-Free 0.284
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Anisotropic B[1][1] -10.1681
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 31.6949
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -21.5268
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5
    Shell Resolution(Low) 3.55
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 3005
    R-Factor(R-Work) 0.3705
    R-Factor(R-Free) 0.3904
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.55
    Shell Resolution(Low) 3.603
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 3180
    R-Factor(R-Work) 0.362
    R-Factor(R-Free) 0.4196
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.603
    Shell Resolution(Low) 3.6592
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 3302
    R-Factor(R-Work) 0.3557
    R-Factor(R-Free) 0.3986
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6592
    Shell Resolution(Low) 3.7192
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 3313
    R-Factor(R-Work) 0.3296
    R-Factor(R-Free) 0.4063
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7192
    Shell Resolution(Low) 3.7833
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 3389
    R-Factor(R-Work) 0.331
    R-Factor(R-Free) 0.3481
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7833
    Shell Resolution(Low) 3.8521
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 3435
    R-Factor(R-Work) 0.3149
    R-Factor(R-Free) 0.3964
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8521
    Shell Resolution(Low) 3.9262
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 3423
    R-Factor(R-Work) 0.3075
    R-Factor(R-Free) 0.3965
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9262
    Shell Resolution(Low) 4.0063
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 3533
    R-Factor(R-Work) 0.3018
    R-Factor(R-Free) 0.3518
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0063
    Shell Resolution(Low) 4.0933
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 3546
    R-Factor(R-Work) 0.2834
    R-Factor(R-Free) 0.3477
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0933
    Shell Resolution(Low) 4.1885
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3545
    R-Factor(R-Work) 0.2678
    R-Factor(R-Free) 0.3475
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1885
    Shell Resolution(Low) 4.2932
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3618
    R-Factor(R-Work) 0.2534
    R-Factor(R-Free) 0.288
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2932
    Shell Resolution(Low) 4.4092
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3610
    R-Factor(R-Work) 0.2261
    R-Factor(R-Free) 0.2559
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4092
    Shell Resolution(Low) 4.5389
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3630
    R-Factor(R-Work) 0.2234
    R-Factor(R-Free) 0.2504
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5389
    Shell Resolution(Low) 4.6853
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3664
    R-Factor(R-Work) 0.2191
    R-Factor(R-Free) 0.2655
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6853
    Shell Resolution(Low) 4.8526
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3667
    R-Factor(R-Work) 0.2112
    R-Factor(R-Free) 0.2131
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8526
    Shell Resolution(Low) 5.0467
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 3650
    R-Factor(R-Work) 0.2189
    R-Factor(R-Free) 0.2643
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0467
    Shell Resolution(Low) 5.2761
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3661
    R-Factor(R-Work) 0.2251
    R-Factor(R-Free) 0.2696
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2761
    Shell Resolution(Low) 5.5539
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3654
    R-Factor(R-Work) 0.2467
    R-Factor(R-Free) 0.3267
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5539
    Shell Resolution(Low) 5.9014
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3674
    R-Factor(R-Work) 0.251
    R-Factor(R-Free) 0.3144
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9014
    Shell Resolution(Low) 6.3562
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3701
    R-Factor(R-Work) 0.2561
    R-Factor(R-Free) 0.2835
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.3562
    Shell Resolution(Low) 6.9943
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3712
    R-Factor(R-Work) 0.2544
    R-Factor(R-Free) 0.283
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.9943
    Shell Resolution(Low) 8.0027
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3693
    R-Factor(R-Work) 0.1956
    R-Factor(R-Free) 0.2555
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.0027
    Shell Resolution(Low) 10.0686
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 3714
    R-Factor(R-Work) 0.1761
    R-Factor(R-Free) 0.2095
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 10.0686
    Shell Resolution(Low) 49.5482
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3692
    R-Factor(R-Work) 0.1915
    R-Factor(R-Free) 0.2589
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 11962
    Nucleic Acid Atoms 12042
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS, HKL2000
    Data Reduction (data scaling) XDS, SCALEPACK
    Structure Solution PHASER, PHENIX
    Structure Refinement PHENIX (PHENIX.REFINE: 1.7_650), CNS 1.3
     
    Software
    refinement CNS version: 1.3
    refinement PHENIX version: (phenix.refine: 1.7_650)
    model building PHENIX
    model building PHASER
    data collection BlueIce