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X-RAY DIFFRACTION
Materials and Methods page
3Q39
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 293.0
    Details 0.1 M Imidazol pH 6.5, 8.25% (w/v) PEG 8000, 1% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 65.12 α = 90
    b = 78.77 β = 99.93
    c = 69.49 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 95
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2010-08-08
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-BM
    Wavelength List 1.0
    Site APS
    Beamline 22-BM
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.25
    Resolution(Low) 28.24
    Number Reflections(All) 190028
    Number Reflections(Observed) 190028
    Percent Possible(Observed) 99.7
    B(Isotropic) From Wilson Plot 9.7
    Redundancy 3.7
     
    High Resolution Shell Details
    Resolution(High) 1.25
    Resolution(Low) 1.28
    Percent Possible(All) 99.7
    Mean I Over Sigma(Observed) 2.33
    R-Sym I(Observed) 0.674
    Redundancy 3.4
    Number Unique Reflections(All) 14021
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.25
    Resolution(Low) 28.24
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 190020
    Number of Reflections(Observed) 190020
    Number of Reflections(R-Free) 9556
    Percent Reflections(Observed) 99.76
    R-Factor(Observed) 0.1689
    R-Work 0.1682
    R-Free 0.182
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic, TLS
    Mean Isotropic B Value 19.617
    Anisotropic B[1][1] -0.6886
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -1.6778
    Anisotropic B[2][2] -0.3199
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.0085
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.25
    Shell Resolution(Low) 1.2642
    Number of Reflections(Observed) 5972
    Number of Reflections(R-Free) 315
    Number of Reflections(R-Work) 5972
    R-Factor(R-Work) 0.2936
    R-Factor(R-Free) 0.2827
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2642
    Shell Resolution(Low) 1.2791
    Number of Reflections(Observed) 6020
    Number of Reflections(R-Free) 309
    Number of Reflections(R-Work) 6020
    R-Factor(R-Work) 0.258
    R-Factor(R-Free) 0.2563
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2791
    Shell Resolution(Low) 1.2947
    Number of Reflections(Observed) 5985
    Number of Reflections(R-Free) 349
    Number of Reflections(R-Work) 5985
    R-Factor(R-Work) 0.2453
    R-Factor(R-Free) 0.2638
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2947
    Shell Resolution(Low) 1.3111
    Number of Reflections(Observed) 6060
    Number of Reflections(R-Free) 275
    Number of Reflections(R-Work) 6060
    R-Factor(R-Work) 0.2291
    R-Factor(R-Free) 0.2429
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3111
    Shell Resolution(Low) 1.3283
    Number of Reflections(Observed) 5979
    Number of Reflections(R-Free) 320
    Number of Reflections(R-Work) 5979
    R-Factor(R-Work) 0.219
    R-Factor(R-Free) 0.2359
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3283
    Shell Resolution(Low) 1.3465
    Number of Reflections(Observed) 5992
    Number of Reflections(R-Free) 300
    Number of Reflections(R-Work) 5992
    R-Factor(R-Work) 0.2168
    R-Factor(R-Free) 0.2218
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3465
    Shell Resolution(Low) 1.3657
    Number of Reflections(Observed) 5981
    Number of Reflections(R-Free) 334
    Number of Reflections(R-Work) 5981
    R-Factor(R-Work) 0.2083
    R-Factor(R-Free) 0.2343
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3657
    Shell Resolution(Low) 1.3861
    Number of Reflections(Observed) 6045
    Number of Reflections(R-Free) 294
    Number of Reflections(R-Work) 6045
    R-Factor(R-Work) 0.1966
    R-Factor(R-Free) 0.2111
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3861
    Shell Resolution(Low) 1.4078
    Number of Reflections(Observed) 5989
    Number of Reflections(R-Free) 315
    Number of Reflections(R-Work) 5989
    R-Factor(R-Work) 0.1909
    R-Factor(R-Free) 0.1897
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4078
    Shell Resolution(Low) 1.4309
    Number of Reflections(Observed) 5976
    Number of Reflections(R-Free) 333
    Number of Reflections(R-Work) 5976
    R-Factor(R-Work) 0.1892
    R-Factor(R-Free) 0.2293
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4309
    Shell Resolution(Low) 1.4555
    Number of Reflections(Observed) 6008
    Number of Reflections(R-Free) 318
    Number of Reflections(R-Work) 6008
    R-Factor(R-Work) 0.1828
    R-Factor(R-Free) 0.215
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4555
    Shell Resolution(Low) 1.482
    Number of Reflections(Observed) 6027
    Number of Reflections(R-Free) 341
    Number of Reflections(R-Work) 6027
    R-Factor(R-Work) 0.1776
    R-Factor(R-Free) 0.1823
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.482
    Shell Resolution(Low) 1.5105
    Number of Reflections(Observed) 5953
    Number of Reflections(R-Free) 339
    Number of Reflections(R-Work) 5953
    R-Factor(R-Work) 0.1675
    R-Factor(R-Free) 0.1991
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5105
    Shell Resolution(Low) 1.5413
    Number of Reflections(Observed) 6010
    Number of Reflections(R-Free) 324
    Number of Reflections(R-Work) 6010
    R-Factor(R-Work) 0.1595
    R-Factor(R-Free) 0.1765
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5413
    Shell Resolution(Low) 1.5749
    Number of Reflections(Observed) 6004
    Number of Reflections(R-Free) 306
    Number of Reflections(R-Work) 6004
    R-Factor(R-Work) 0.1557
    R-Factor(R-Free) 0.1695
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5749
    Shell Resolution(Low) 1.6115
    Number of Reflections(Observed) 6029
    Number of Reflections(R-Free) 321
    Number of Reflections(R-Work) 6029
    R-Factor(R-Work) 0.1539
    R-Factor(R-Free) 0.186
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6115
    Shell Resolution(Low) 1.6518
    Number of Reflections(Observed) 5971
    Number of Reflections(R-Free) 336
    Number of Reflections(R-Work) 5971
    R-Factor(R-Work) 0.1575
    R-Factor(R-Free) 0.1915
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6518
    Shell Resolution(Low) 1.6964
    Number of Reflections(Observed) 6017
    Number of Reflections(R-Free) 336
    Number of Reflections(R-Work) 6017
    R-Factor(R-Work) 0.1537
    R-Factor(R-Free) 0.1664
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6964
    Shell Resolution(Low) 1.7464
    Number of Reflections(Observed) 6045
    Number of Reflections(R-Free) 282
    Number of Reflections(R-Work) 6045
    R-Factor(R-Work) 0.1504
    R-Factor(R-Free) 0.1537
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7464
    Shell Resolution(Low) 1.8027
    Number of Reflections(Observed) 5998
    Number of Reflections(R-Free) 322
    Number of Reflections(R-Work) 5998
    R-Factor(R-Work) 0.1487
    R-Factor(R-Free) 0.1708
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8027
    Shell Resolution(Low) 1.8671
    Number of Reflections(Observed) 5986
    Number of Reflections(R-Free) 331
    Number of Reflections(R-Work) 5986
    R-Factor(R-Work) 0.1492
    R-Factor(R-Free) 0.1537
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8671
    Shell Resolution(Low) 1.9419
    Number of Reflections(Observed) 6008
    Number of Reflections(R-Free) 337
    Number of Reflections(R-Work) 6008
    R-Factor(R-Work) 0.1558
    R-Factor(R-Free) 0.177
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9419
    Shell Resolution(Low) 2.0302
    Number of Reflections(Observed) 6047
    Number of Reflections(R-Free) 310
    Number of Reflections(R-Work) 6047
    R-Factor(R-Work) 0.1532
    R-Factor(R-Free) 0.1677
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0302
    Shell Resolution(Low) 2.1372
    Number of Reflections(Observed) 6017
    Number of Reflections(R-Free) 296
    Number of Reflections(R-Work) 6017
    R-Factor(R-Work) 0.1493
    R-Factor(R-Free) 0.16
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1372
    Shell Resolution(Low) 2.2711
    Number of Reflections(Observed) 6042
    Number of Reflections(R-Free) 321
    Number of Reflections(R-Work) 6042
    R-Factor(R-Work) 0.1579
    R-Factor(R-Free) 0.17
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2711
    Shell Resolution(Low) 2.4463
    Number of Reflections(Observed) 5987
    Number of Reflections(R-Free) 348
    Number of Reflections(R-Work) 5987
    R-Factor(R-Work) 0.1572
    R-Factor(R-Free) 0.1763
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4463
    Shell Resolution(Low) 2.6923
    Number of Reflections(Observed) 6059
    Number of Reflections(R-Free) 311
    Number of Reflections(R-Work) 6059
    R-Factor(R-Work) 0.1658
    R-Factor(R-Free) 0.1695
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6923
    Shell Resolution(Low) 3.0815
    Number of Reflections(Observed) 6049
    Number of Reflections(R-Free) 309
    Number of Reflections(R-Work) 6049
    R-Factor(R-Work) 0.1723
    R-Factor(R-Free) 0.1851
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0815
    Shell Resolution(Low) 3.8808
    Number of Reflections(Observed) 6074
    Number of Reflections(R-Free) 317
    Number of Reflections(R-Work) 6074
    R-Factor(R-Work) 0.1606
    R-Factor(R-Free) 0.1766
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8808
    Shell Resolution(Low) 28.2475
    Number of Reflections(Observed) 6134
    Number of Reflections(R-Free) 307
    Number of Reflections(R-Work) 6134
    R-Factor(R-Work) 0.1644
    R-Factor(R-Free) 0.171
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.011
    f_chiral_restr 0.121
    f_dihedral_angle_d 13.021
    f_angle_d 1.758
    f_bond_d 0.018
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4814
    Nucleic Acid Atoms 0
    Heterogen Atoms 130
    Solvent Atoms 803
     
     
  •   Software and Computing Hide
    Computing
    Data Collection SERGUI
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER (2.1.4)
    Structure Refinement PHENIX (phenix.refine: 1.6.4_486)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.6.4_486)
    model building PHASER version: (2.1.4)
    data collection SERGUI