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X-RAY DIFFRACTION
Materials and Methods page
3V6U
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7
    Temperature 293.0
    Details 3.5-4.5% PEG 20K, 3.5-4.5% PEG550 MME, 0.1M TRIS-ACETATE, 0.2M KSCN, 10MM MGCL2, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 210.2 α = 90
    b = 446.16 β = 90
    c = 620.95 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Details MIRRORS
    Collection Date 2011-07-22
     
    Diffraction Radiation
    Monochromator KOHZU DIAMOND MONOCHROMATOR
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.97
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.9
    Resolution(Low) 50
    Number Reflections(Observed) 497544
    Percent Possible(Observed) 94.3
    R Merge I(Observed) 0.354
    Redundancy 6.6
     
    High Resolution Shell Details
    Resolution(High) 3.9
    Resolution(Low) 4.1
    Percent Possible(All) 90.9
    R Merge I(Observed) 1.409
    Mean I Over Sigma(Observed) 1.8
    Redundancy 6.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.9
    Resolution(Low) 50.0
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 526847
    Number of Reflections(Observed) 496744
    Number of Reflections(R-Free) 22067
    Percent Reflections(Observed) 94.34
    R-Factor(Observed) 0.2432
    R-Work 0.242
    R-Free 0.2692
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -7.704
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 7.0673
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 23.1822
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9
    Shell Resolution(Low) 3.9443
    Number of Reflections(R-Free) 625
    Number of Reflections(R-Work) 11959
    R-Factor(R-Work) 0.3445
    R-Factor(R-Free) 0.3643
    Percent Reflections(Observed) 72.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9443
    Shell Resolution(Low) 3.9907
    Number of Reflections(R-Free) 814
    Number of Reflections(R-Work) 15837
    R-Factor(R-Work) 0.3002
    R-Factor(R-Free) 0.3407
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9907
    Shell Resolution(Low) 4.0393
    Number of Reflections(R-Free) 833
    Number of Reflections(R-Work) 15876
    R-Factor(R-Work) 0.3002
    R-Factor(R-Free) 0.3359
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0393
    Shell Resolution(Low) 4.0904
    Number of Reflections(R-Free) 828
    Number of Reflections(R-Work) 15746
    R-Factor(R-Work) 0.2928
    R-Factor(R-Free) 0.3083
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0904
    Shell Resolution(Low) 4.1442
    Number of Reflections(R-Free) 834
    Number of Reflections(R-Work) 15800
    R-Factor(R-Work) 0.2854
    R-Factor(R-Free) 0.2846
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1442
    Shell Resolution(Low) 4.201
    Number of Reflections(R-Free) 844
    Number of Reflections(R-Work) 15844
    R-Factor(R-Work) 0.2845
    R-Factor(R-Free) 0.3255
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.201
    Shell Resolution(Low) 4.261
    Number of Reflections(R-Free) 824
    Number of Reflections(R-Work) 15689
    R-Factor(R-Work) 0.277
    R-Factor(R-Free) 0.306
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.261
    Shell Resolution(Low) 4.3245
    Number of Reflections(R-Free) 833
    Number of Reflections(R-Work) 15722
    R-Factor(R-Work) 0.2685
    R-Factor(R-Free) 0.2959
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3245
    Shell Resolution(Low) 4.3921
    Number of Reflections(R-Free) 819
    Number of Reflections(R-Work) 15761
    R-Factor(R-Work) 0.2635
    R-Factor(R-Free) 0.2816
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3921
    Shell Resolution(Low) 4.464
    Number of Reflections(R-Free) 496
    Number of Reflections(R-Work) 16131
    R-Factor(R-Work) 0.2627
    R-Factor(R-Free) 0.2679
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.464
    Shell Resolution(Low) 4.5409
    Number of Reflections(R-Free) 444
    Number of Reflections(R-Work) 16036
    R-Factor(R-Work) 0.2529
    R-Factor(R-Free) 0.2659
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5409
    Shell Resolution(Low) 4.6235
    Number of Reflections(R-Free) 490
    Number of Reflections(R-Work) 16009
    R-Factor(R-Work) 0.2558
    R-Factor(R-Free) 0.2647
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6235
    Shell Resolution(Low) 4.7123
    Number of Reflections(R-Free) 553
    Number of Reflections(R-Work) 15989
    R-Factor(R-Work) 0.2486
    R-Factor(R-Free) 0.2691
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7123
    Shell Resolution(Low) 4.8084
    Number of Reflections(R-Free) 619
    Number of Reflections(R-Work) 15863
    R-Factor(R-Work) 0.2473
    R-Factor(R-Free) 0.2699
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8084
    Shell Resolution(Low) 4.9129
    Number of Reflections(R-Free) 719
    Number of Reflections(R-Work) 15680
    R-Factor(R-Work) 0.2457
    R-Factor(R-Free) 0.2724
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9129
    Shell Resolution(Low) 5.0271
    Number of Reflections(R-Free) 825
    Number of Reflections(R-Work) 15706
    R-Factor(R-Work) 0.2465
    R-Factor(R-Free) 0.2722
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0271
    Shell Resolution(Low) 5.1527
    Number of Reflections(R-Free) 816
    Number of Reflections(R-Work) 15599
    R-Factor(R-Work) 0.2324
    R-Factor(R-Free) 0.268
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1527
    Shell Resolution(Low) 5.2918
    Number of Reflections(R-Free) 812
    Number of Reflections(R-Work) 15614
    R-Factor(R-Work) 0.2292
    R-Factor(R-Free) 0.2526
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2918
    Shell Resolution(Low) 5.4474
    Number of Reflections(R-Free) 815
    Number of Reflections(R-Work) 15709
    R-Factor(R-Work) 0.2208
    R-Factor(R-Free) 0.2552
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4474
    Shell Resolution(Low) 5.6229
    Number of Reflections(R-Free) 818
    Number of Reflections(R-Work) 15848
    R-Factor(R-Work) 0.2254
    R-Factor(R-Free) 0.2544
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.6229
    Shell Resolution(Low) 5.8236
    Number of Reflections(R-Free) 809
    Number of Reflections(R-Work) 15964
    R-Factor(R-Work) 0.2286
    R-Factor(R-Free) 0.266
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.8236
    Shell Resolution(Low) 6.0564
    Number of Reflections(R-Free) 828
    Number of Reflections(R-Work) 16036
    R-Factor(R-Work) 0.2269
    R-Factor(R-Free) 0.2558
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.0564
    Shell Resolution(Low) 6.3315
    Number of Reflections(R-Free) 847
    Number of Reflections(R-Work) 16197
    R-Factor(R-Work) 0.2317
    R-Factor(R-Free) 0.2687
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.3315
    Shell Resolution(Low) 6.6646
    Number of Reflections(R-Free) 837
    Number of Reflections(R-Work) 16273
    R-Factor(R-Work) 0.2344
    R-Factor(R-Free) 0.2711
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6646
    Shell Resolution(Low) 7.081
    Number of Reflections(R-Free) 674
    Number of Reflections(R-Work) 16379
    R-Factor(R-Work) 0.2191
    R-Factor(R-Free) 0.2506
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.081
    Shell Resolution(Low) 7.6259
    Number of Reflections(R-Free) 541
    Number of Reflections(R-Work) 16474
    R-Factor(R-Work) 0.2153
    R-Factor(R-Free) 0.248
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.6259
    Shell Resolution(Low) 8.39
    Number of Reflections(R-Free) 614
    Number of Reflections(R-Work) 16428
    R-Factor(R-Work) 0.2162
    R-Factor(R-Free) 0.2457
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.39
    Shell Resolution(Low) 9.5963
    Number of Reflections(R-Free) 687
    Number of Reflections(R-Work) 16287
    R-Factor(R-Work) 0.2174
    R-Factor(R-Free) 0.2421
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.5963
    Shell Resolution(Low) 12.0614
    Number of Reflections(R-Free) 770
    Number of Reflections(R-Work) 16280
    R-Factor(R-Work) 0.2104
    R-Factor(R-Free) 0.2304
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 12.0614
    Shell Resolution(Low) 49.4719
    Number of Reflections(R-Free) 799
    Number of Reflections(R-Work) 15941
    R-Factor(R-Work) 0.2382
    R-Factor(R-Free) 0.2556
    Percent Reflections(Observed) 91.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.012
    f_chiral_restr 0.086
    f_dihedral_angle_d 17.354
    f_angle_d 1.203
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19156
    Nucleic Acid Atoms 36123
    Heterogen Atoms 412
    Solvent Atoms 0
     
     
  •   Software and Computing Hide
    Computing
    Data Collection XDS
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHENIX (phenix.refine: 1.7_641)
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement REFMAC5