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X-RAY DIFFRACTION
Materials and Methods page
3W1J
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.5
    Temperature 293.0
    Details 120mM Tris-HCl, 12% PEG 4000, 800mM NaNO3, 160mM KCl, 50mM L-serine, 50mM Na2S2O3, 0.2M NaCl, 10mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 92.44 α = 102.09
    b = 116.37 β = 93.39
    c = 124.79 γ = 106.06
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 90
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Details mirrors
    Collection Date 2007-05-31
     
    Diffraction Radiation
    Monochromator Si
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE BL-5A
    Wavelength List 1.00000
    Site PHOTON FACTORY
    Beamline BL-5A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -2.0
    Resolution(High) 3.25
    Resolution(Low) 50
    Number Reflections(All) 76007
    Number Reflections(Observed) 75475
    Percent Possible(Observed) 99.3
    R Merge I(Observed) 0.129
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 3.25
    Resolution(Low) 3.37
    Percent Possible(All) 98.6
    R Merge I(Observed) 0.538
    Mean I Over Sigma(Observed) 2.05
    R-Sym I(Observed) 0.538
    Redundancy 3.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.252
    Resolution(Low) 38.518
    Cut-off Sigma(F) 1.97
    Number of Reflections(all) 76178
    Number of Reflections(Observed) 75371
    Number of Reflections(R-Free) 3812
    Percent Reflections(Observed) 98.94
    R-Factor(Observed) 0.2036
    R-Work 0.2003
    R-Free 0.2661
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 123.292
    Anisotropic B[1][1] -40.2921
    Anisotropic B[1][2] -0.5608
    Anisotropic B[1][3] -7.5529
    Anisotropic B[2][2] 41.1022
    Anisotropic B[2][3] -2.4413
    Anisotropic B[3][3] -0.8101
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2523
    Shell Resolution(Low) 3.2934
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2501
    R-Factor(R-Work) 0.3399
    R-Factor(R-Free) 0.4392
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2934
    Shell Resolution(Low) 3.3367
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2631
    R-Factor(R-Work) 0.316
    R-Factor(R-Free) 0.3613
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3367
    Shell Resolution(Low) 3.3824
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 2624
    R-Factor(R-Work) 0.2973
    R-Factor(R-Free) 0.3814
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3824
    Shell Resolution(Low) 3.4307
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2699
    R-Factor(R-Work) 0.2634
    R-Factor(R-Free) 0.3467
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4307
    Shell Resolution(Low) 3.4819
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2591
    R-Factor(R-Work) 0.2656
    R-Factor(R-Free) 0.3184
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4819
    Shell Resolution(Low) 3.5363
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2711
    R-Factor(R-Work) 0.2558
    R-Factor(R-Free) 0.3413
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5363
    Shell Resolution(Low) 3.5942
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2597
    R-Factor(R-Work) 0.2498
    R-Factor(R-Free) 0.3097
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5942
    Shell Resolution(Low) 3.6561
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2689
    R-Factor(R-Work) 0.2322
    R-Factor(R-Free) 0.2958
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6561
    Shell Resolution(Low) 3.7226
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.233
    R-Factor(R-Free) 0.3173
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7226
    Shell Resolution(Low) 3.7941
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.2278
    R-Factor(R-Free) 0.3196
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7941
    Shell Resolution(Low) 3.8715
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2668
    R-Factor(R-Work) 0.2162
    R-Factor(R-Free) 0.2706
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8715
    Shell Resolution(Low) 3.9556
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2628
    R-Factor(R-Work) 0.2042
    R-Factor(R-Free) 0.2534
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9556
    Shell Resolution(Low) 4.0475
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2654
    R-Factor(R-Work) 0.1938
    R-Factor(R-Free) 0.27
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0475
    Shell Resolution(Low) 4.1486
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.1818
    R-Factor(R-Free) 0.2366
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1486
    Shell Resolution(Low) 4.2606
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.1785
    R-Factor(R-Free) 0.262
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2606
    Shell Resolution(Low) 4.3858
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2691
    R-Factor(R-Work) 0.1664
    R-Factor(R-Free) 0.2612
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3858
    Shell Resolution(Low) 4.5272
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.1593
    R-Factor(R-Free) 0.2177
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5272
    Shell Resolution(Low) 4.6887
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2695
    R-Factor(R-Work) 0.1493
    R-Factor(R-Free) 0.2245
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6887
    Shell Resolution(Low) 4.8761
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2670
    R-Factor(R-Work) 0.1483
    R-Factor(R-Free) 0.2298
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8761
    Shell Resolution(Low) 5.0975
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2640
    R-Factor(R-Work) 0.1583
    R-Factor(R-Free) 0.253
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0975
    Shell Resolution(Low) 5.3656
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2677
    R-Factor(R-Work) 0.1658
    R-Factor(R-Free) 0.2309
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3656
    Shell Resolution(Low) 5.7008
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2649
    R-Factor(R-Work) 0.1998
    R-Factor(R-Free) 0.3042
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7008
    Shell Resolution(Low) 6.1393
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.2032
    R-Factor(R-Free) 0.2975
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.1393
    Shell Resolution(Low) 6.7542
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.2278
    R-Factor(R-Free) 0.3148
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.7542
    Shell Resolution(Low) 7.7247
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2672
    R-Factor(R-Work) 0.1794
    R-Factor(R-Free) 0.2604
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.7247
    Shell Resolution(Low) 9.7065
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2672
    R-Factor(R-Work) 0.1435
    R-Factor(R-Free) 0.1816
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.7065
    Shell Resolution(Low) 38.5209
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2646
    R-Factor(R-Work) 0.2429
    R-Factor(R-Free) 0.2453
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.109
    f_plane_restr 0.004
    f_chiral_restr 0.074
    f_angle_d 1.26
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 30803
    Nucleic Acid Atoms 0
    Heterogen Atoms 85
    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: 1.7.1_743)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction HKL