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X-RAY DIFFRACTION
Materials and Methods page
3V9Z
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.5
    Temperature 298.0
    Details 0.1M Sodium acetate trihydrate, 10%(w/v) Polyethylene glycol 1000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 96.42 α = 90
    b = 106.09 β = 90
    c = 46.95 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX225HE
    Collection Date 2010-11-15
     
    Diffraction Radiation
    Monochromator SAGITALLY FOCUSED Si(III)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL44XU
    Wavelength List 0.9
    Site SPRING-8
    Beamline BL44XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.8
    Resolution(Low) 30
    Number Reflections(All) 44147
    Number Reflections(Observed) 44147
    Percent Possible(Observed) 96.4
    Redundancy 5.4
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.83
    Percent Possible(All) 100.0
    Mean I Over Sigma(Observed) 8.6
    R-Sym I(Observed) 0.362
    Redundancy 5.8
    Number Unique Reflections(All) 2239
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 28.515
    Cut-off Sigma(F) 1.33
    Number of Reflections(all) 43648
    Number of Reflections(Observed) 43648
    Number of Reflections(R-Free) 2201
    Percent Reflections(Observed) 96.0
    R-Factor(Observed) 0.2128
    R-Work 0.211
    R-Free 0.2475
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 17.7143
    Anisotropic B[1][1] 1.8496
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.8387
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.0109
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.8391
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.2417
    R-Factor(R-Free) 0.3105
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8391
    Shell Resolution(Low) 1.8819
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.2377
    R-Factor(R-Free) 0.2801
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8819
    Shell Resolution(Low) 1.929
    Number of Reflections(R-Free) 101
    Number of Reflections(R-Work) 2020
    R-Factor(R-Work) 0.368
    R-Factor(R-Free) 0.4615
    Percent Reflections(Observed) 77.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.929
    Shell Resolution(Low) 1.9811
    Number of Reflections(R-Free) 113
    Number of Reflections(R-Work) 2545
    R-Factor(R-Work) 0.2303
    R-Factor(R-Free) 0.3127
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9811
    Shell Resolution(Low) 2.0394
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2678
    R-Factor(R-Work) 0.1873
    R-Factor(R-Free) 0.2106
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0394
    Shell Resolution(Low) 2.1052
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2642
    R-Factor(R-Work) 0.1889
    R-Factor(R-Free) 0.2402
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1052
    Shell Resolution(Low) 2.1804
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.1982
    R-Factor(R-Free) 0.2355
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1804
    Shell Resolution(Low) 2.2677
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2206
    R-Factor(R-Work) 0.2542
    R-Factor(R-Free) 0.3051
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2677
    Shell Resolution(Low) 2.3708
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2538
    R-Factor(R-Work) 0.2056
    R-Factor(R-Free) 0.2363
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3708
    Shell Resolution(Low) 2.4958
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.1927
    R-Factor(R-Free) 0.2392
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4958
    Shell Resolution(Low) 2.652
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2700
    R-Factor(R-Work) 0.215
    R-Factor(R-Free) 0.2838
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.652
    Shell Resolution(Low) 2.8566
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.2149
    R-Factor(R-Free) 0.2419
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8566
    Shell Resolution(Low) 3.1438
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2703
    R-Factor(R-Work) 0.2065
    R-Factor(R-Free) 0.2203
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1438
    Shell Resolution(Low) 3.5979
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2693
    R-Factor(R-Work) 0.1944
    R-Factor(R-Free) 0.2335
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5979
    Shell Resolution(Low) 4.5301
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2634
    R-Factor(R-Work) 0.1792
    R-Factor(R-Free) 0.228
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5301
    Shell Resolution(Low) 28.5187
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 2777
    R-Factor(R-Work) 0.2111
    R-Factor(R-Free) 0.205
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.587
    f_plane_restr 0.004
    f_chiral_restr 0.075
    f_angle_d 1.0
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3218
    Nucleic Acid Atoms 118
    Heterogen Atoms 3
    Solvent Atoms 632
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution AMoRE
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building AMoRE
    data collection HKL-2000