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X-RAY DIFFRACTION
Materials and Methods page
3WQY
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6
    Temperature 293.0
    Details PEG 6000, citrate buffer, CdCl2, MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 99.74 α = 90
    b = 169.84 β = 90
    c = 175.26 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 90
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX225HE
    Collection Date 2012-11-14
     
    Diffraction Radiation
    Monochromator Si
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL41XU
    Wavelength List 1.0
    Site SPRING-8
    Beamline BL41XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -1.0
    Resolution(High) 3.3
    Resolution(Low) 50
    Number Reflections(All) 45965
    Number Reflections(Observed) 45365
    Percent Possible(Observed) 99.6
    Redundancy 5.4
     
    High Resolution Shell Details
    Resolution(High) 3.3
    Resolution(Low) 3.42
    Percent Possible(All) 99.3
    R Merge I(Observed) 0.654
    Mean I Over Sigma(Observed) 2.25
    R-Sym I(Observed) 0.654
    Redundancy 4.2
    Number Unique Reflections(All) 4570
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.3
    Resolution(Low) 41.765
    Cut-off Sigma(F) 1.38
    Number of Reflections(Observed) 45304
    Number of Reflections(R-Free) 2329
    Percent Reflections(Observed) 99.48
    R-Factor(Observed) 0.2523
    R-Work 0.2503
    R-Free 0.2893
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 96.88
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2989
    Shell Resolution(Low) 3.3662
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 2432
    R-Factor(R-Work) 0.3775
    R-Factor(R-Free) 0.3899
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3662
    Shell Resolution(Low) 3.4394
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2511
    R-Factor(R-Work) 0.3547
    R-Factor(R-Free) 0.3628
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4394
    Shell Resolution(Low) 3.5194
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2455
    R-Factor(R-Work) 0.3544
    R-Factor(R-Free) 0.3593
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5194
    Shell Resolution(Low) 3.6073
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2488
    R-Factor(R-Work) 0.3325
    R-Factor(R-Free) 0.3331
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6073
    Shell Resolution(Low) 3.7048
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2507
    R-Factor(R-Work) 0.3203
    R-Factor(R-Free) 0.3822
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7048
    Shell Resolution(Low) 3.8137
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2510
    R-Factor(R-Work) 0.2981
    R-Factor(R-Free) 0.3287
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8137
    Shell Resolution(Low) 3.9368
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2516
    R-Factor(R-Work) 0.2845
    R-Factor(R-Free) 0.331
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9368
    Shell Resolution(Low) 4.0773
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2480
    R-Factor(R-Work) 0.2703
    R-Factor(R-Free) 0.2933
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0773
    Shell Resolution(Low) 4.2404
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2494
    R-Factor(R-Work) 0.2466
    R-Factor(R-Free) 0.3323
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2404
    Shell Resolution(Low) 4.4332
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2516
    R-Factor(R-Work) 0.2406
    R-Factor(R-Free) 0.2977
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4332
    Shell Resolution(Low) 4.6667
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2523
    R-Factor(R-Work) 0.2243
    R-Factor(R-Free) 0.2405
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6667
    Shell Resolution(Low) 4.9586
    Number of Reflections(R-Free) 115
    Number of Reflections(R-Work) 2569
    R-Factor(R-Work) 0.2065
    R-Factor(R-Free) 0.2464
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9586
    Shell Resolution(Low) 5.3408
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2546
    R-Factor(R-Work) 0.219
    R-Factor(R-Free) 0.2676
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3408
    Shell Resolution(Low) 5.8769
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2551
    R-Factor(R-Work) 0.2364
    R-Factor(R-Free) 0.2637
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8769
    Shell Resolution(Low) 6.7243
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2563
    R-Factor(R-Work) 0.2495
    R-Factor(R-Free) 0.2668
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.7243
    Shell Resolution(Low) 8.4603
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2605
    R-Factor(R-Work) 0.2167
    R-Factor(R-Free) 0.2726
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.4603
    Shell Resolution(Low) 41.7678
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2709
    R-Factor(R-Work) 0.1821
    R-Factor(R-Free) 0.2298
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.015
    f_chiral_restr 0.035
    f_dihedral_angle_d 15.879
    f_angle_d 0.886
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 14421
    Nucleic Acid Atoms 1609
    Heterogen Atoms 59
    Solvent Atoms 7
     
     
  •   Software and Computing Hide
    Computing
    Structure Refinement PHENIX (phenix.refine: 1.8.4_1496)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.4_1496)