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X-RAY DIFFRACTION
Materials and Methods page
4JJN
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 277.0
    Details 0.05 M sodium cacodylate, 32% 2-methyl-2,4-pentanediol (MPD), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 103.68 α = 90
    b = 103.68 β = 90
    c = 556.38 γ = 120
     
    Space Group
    Space Group Name:    P 61
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type PSI PILATUS 6M
    Collection Date 2012-08-15
     
    Diffraction Radiation
    Monochromator SAGITALLY FOCUSED Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.97920
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.09
    Resolution(Low) 139.09
    Number Reflections(All) 61627
    Number Reflections(Observed) 60025
    Percent Possible(Observed) 97.4
    R Merge I(Observed) 0.039
    Redundancy 2.9
     
    High Resolution Shell Details
    Resolution(High) 3.09
    Resolution(Low) 3.26
    Percent Possible(All) 97.9
    R Merge I(Observed) 0.487
    Mean I Over Sigma(Observed) 1.5
    R-Sym I(Observed) 0.487
    Redundancy 2.9
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.09
    Resolution(Low) 85.45
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 61484
    Number of Reflections(Observed) 59664
    Number of Reflections(R-Free) 3025
    Percent Reflections(Observed) 97.04
    R-Factor(Observed) 0.2325
    R-Work 0.2313
    R-Free 0.2548
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 78.24
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.09
    Shell Resolution(Low) 3.1391
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2448
    R-Factor(R-Work) 0.356
    R-Factor(R-Free) 0.3427
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1391
    Shell Resolution(Low) 3.1906
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2591
    R-Factor(R-Work) 0.3425
    R-Factor(R-Free) 0.3251
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1906
    Shell Resolution(Low) 3.2456
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.3382
    R-Factor(R-Free) 0.3846
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2456
    Shell Resolution(Low) 3.3046
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2545
    R-Factor(R-Work) 0.3217
    R-Factor(R-Free) 0.3957
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3046
    Shell Resolution(Low) 3.3682
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2577
    R-Factor(R-Work) 0.3071
    R-Factor(R-Free) 0.357
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3682
    Shell Resolution(Low) 3.437
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2575
    R-Factor(R-Work) 0.2988
    R-Factor(R-Free) 0.2857
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.437
    Shell Resolution(Low) 3.5117
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2512
    R-Factor(R-Work) 0.2834
    R-Factor(R-Free) 0.293
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5117
    Shell Resolution(Low) 3.5934
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2694
    R-Factor(R-Work) 0.262
    R-Factor(R-Free) 0.3181
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5934
    Shell Resolution(Low) 3.6832
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2648
    R-Factor(R-Work) 0.2568
    R-Factor(R-Free) 0.293
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6832
    Shell Resolution(Low) 3.7828
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2614
    R-Factor(R-Work) 0.2665
    R-Factor(R-Free) 0.3051
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7828
    Shell Resolution(Low) 3.8941
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2655
    R-Factor(R-Work) 0.2621
    R-Factor(R-Free) 0.3134
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8941
    Shell Resolution(Low) 4.0198
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2633
    R-Factor(R-Work) 0.2539
    R-Factor(R-Free) 0.2937
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0198
    Shell Resolution(Low) 4.1635
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.2446
    R-Factor(R-Free) 0.2655
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1635
    Shell Resolution(Low) 4.3302
    Number of Reflections(R-Free) 113
    Number of Reflections(R-Work) 2575
    R-Factor(R-Work) 0.2398
    R-Factor(R-Free) 0.29
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3302
    Shell Resolution(Low) 4.5273
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2509
    R-Factor(R-Work) 0.2357
    R-Factor(R-Free) 0.2671
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5273
    Shell Resolution(Low) 4.7659
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2538
    R-Factor(R-Work) 0.2227
    R-Factor(R-Free) 0.2603
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7659
    Shell Resolution(Low) 5.0645
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.219
    R-Factor(R-Free) 0.2299
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0645
    Shell Resolution(Low) 5.4555
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.232
    R-Factor(R-Free) 0.2402
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4555
    Shell Resolution(Low) 6.0044
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2556
    R-Factor(R-Work) 0.2407
    R-Factor(R-Free) 0.2711
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0044
    Shell Resolution(Low) 6.8729
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2423
    R-Factor(R-Work) 0.2468
    R-Factor(R-Free) 0.2839
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.8729
    Shell Resolution(Low) 8.6578
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2583
    R-Factor(R-Work) 0.1926
    R-Factor(R-Free) 0.185
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.6578
    Shell Resolution(Low) 85.483
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2415
    R-Factor(R-Work) 0.161
    R-Factor(R-Free) 0.1693
    Percent Reflections(Observed) 90.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.002
    f_chiral_restr 0.033
    f_dihedral_angle_d 21.316
    f_angle_d 0.611
    f_bond_d 0.002
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9635
    Nucleic Acid Atoms 5986
    Heterogen Atoms 0
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution Phaser (CCP4-6.1.1)
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8_1069)
    model building Phaser version: (CCP4-6.1.1)
    data collection ADSC version: Quantum