POP-OUT | CLOSE

An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4GXH
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.2
    Temperature 293.0
    Details 0.2 M Na2HPO4/KH2PO4, 2.5 M Sodium Chloride, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 117.18 α = 90
    b = 117.18 β = 90
    c = 186.62 γ = 90
     
    Space Group
    Space Group Name:    P 43 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 77
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-04-27
     
    Diffraction Radiation
    Monochromator ROSENBAUM-ROCK DOUBLE CRYSTAL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 1.075
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 2.7
    Resolution(Low) 50
    Number Reflections(All) 68317
    Number Reflections(Observed) 40725
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.091
    B(Isotropic) From Wilson Plot 59.83
    Redundancy 5.3
     
    High Resolution Shell Details
    Resolution(High) 2.7
    Resolution(Low) 2.75
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.89
    Redundancy 5.3
    Number Unique Reflections(All) 3433
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.7
    Resolution(Low) 45.691
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 40725
    Number of Reflections(Observed) 36353
    Number of Reflections(R-Free) 1821
    Percent Reflections(Observed) 99.77
    R-Factor(Observed) 0.1782
    R-Work 0.176
    R-Free 0.219
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 47.7633
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7001
    Shell Resolution(Low) 2.7731
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2598
    R-Factor(R-Work) 0.2443
    R-Factor(R-Free) 0.2907
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7731
    Shell Resolution(Low) 2.8547
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2631
    R-Factor(R-Work) 0.2586
    R-Factor(R-Free) 0.2816
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8547
    Shell Resolution(Low) 2.9468
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2599
    R-Factor(R-Work) 0.2484
    R-Factor(R-Free) 0.3236
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9468
    Shell Resolution(Low) 3.0521
    Number of Reflections(R-Free) 112
    Number of Reflections(R-Work) 2632
    R-Factor(R-Work) 0.2351
    R-Factor(R-Free) 0.2727
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0521
    Shell Resolution(Low) 3.1742
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2623
    R-Factor(R-Work) 0.2246
    R-Factor(R-Free) 0.3076
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1742
    Shell Resolution(Low) 3.3187
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2636
    R-Factor(R-Work) 0.2147
    R-Factor(R-Free) 0.2717
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3187
    Shell Resolution(Low) 3.4936
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2615
    R-Factor(R-Work) 0.1947
    R-Factor(R-Free) 0.2279
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4936
    Shell Resolution(Low) 3.7124
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.1813
    R-Factor(R-Free) 0.2152
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7124
    Shell Resolution(Low) 3.9989
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.1628
    R-Factor(R-Free) 0.2254
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9989
    Shell Resolution(Low) 4.401
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.1402
    R-Factor(R-Free) 0.197
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.401
    Shell Resolution(Low) 5.0371
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2671
    R-Factor(R-Work) 0.1289
    R-Factor(R-Free) 0.1638
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0371
    Shell Resolution(Low) 6.3435
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2724
    R-Factor(R-Work) 0.1601
    R-Factor(R-Free) 0.186
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.3435
    Shell Resolution(Low) 45.6976
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2852
    R-Factor(R-Work) 0.1678
    R-Factor(R-Free) 0.2003
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.908
    f_plane_restr 0.007
    f_chiral_restr 0.081
    f_angle_d 1.383
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6154
    Nucleic Acid Atoms 0
    Heterogen Atoms 29
    Solvent Atoms 96
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    Data Reduction (intensity integration) HKL-3000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MOLREP
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement MOLREP
    data reduction SCALEPACK