POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4ISD
  •   Crystallization Hide
    Crystallization Experiments
    Method sitting drop vapor diffusion
    pH 7
    Temperature 298.0
    Details Protein (10 mM Hepes pH 7.5, 25 mM NaCl, 5 mM Reduced glutathione), Reservoir (25% Sokalan CP7, 0.1 M KCl, 0.1 M HEPES pH 7), Cryoprotection (reservoir + 20% glycerol), sitting drop vapor diffusion, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 56 α = 90
    b = 196.34 β = 90
    c = 275.36 γ = 90
     
    Space Group
    Space Group Name:    C 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-225
    Details MIRRORS
    Collection Date 2012-08-13
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 31-ID
    Wavelength List 0.9793
    Site APS
    Beamline 31-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.65
    Resolution(Low) 275.36
    Number Reflections(All) 43996
    Number Reflections(Observed) 43996
    Percent Possible(Observed) 98.5
    R Merge I(Observed) 0.095
    Redundancy 15.0
     
    High Resolution Shell Details
    Resolution(High) 2.65
    Resolution(Low) 2.79
    Percent Possible(All) 98.2
    R Merge I(Observed) 0.869
    Mean I Over Sigma(Observed) 0.9
    R-Sym I(Observed) 0.869
    Redundancy 15.3
    Number Unique Reflections(All) 6328
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.65
    Resolution(Low) 92.47
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 43896
    Number of Reflections(Observed) 43896
    Number of Reflections(R-Free) 2228
    Percent Reflections(Observed) 97.94
    R-Factor(All) 0.201
    R-Factor(Observed) 0.201
    R-Work 0.1981
    R-Free 0.2543
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 61.9006
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.65
    Shell Resolution(Low) 2.7076
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2553
    R-Factor(R-Work) 0.261
    R-Factor(R-Free) 0.326
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7076
    Shell Resolution(Low) 2.7706
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2566
    R-Factor(R-Work) 0.245
    R-Factor(R-Free) 0.3342
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7706
    Shell Resolution(Low) 2.8399
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2578
    R-Factor(R-Work) 0.2312
    R-Factor(R-Free) 0.258
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8399
    Shell Resolution(Low) 2.9167
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2568
    R-Factor(R-Work) 0.2253
    R-Factor(R-Free) 0.2814
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9167
    Shell Resolution(Low) 3.0025
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2597
    R-Factor(R-Work) 0.2257
    R-Factor(R-Free) 0.3283
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0025
    Shell Resolution(Low) 3.0994
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2566
    R-Factor(R-Work) 0.2085
    R-Factor(R-Free) 0.3007
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0994
    Shell Resolution(Low) 3.2101
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2525
    R-Factor(R-Work) 0.2078
    R-Factor(R-Free) 0.2658
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2101
    Shell Resolution(Low) 3.3386
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2602
    R-Factor(R-Work) 0.2113
    R-Factor(R-Free) 0.2714
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3386
    Shell Resolution(Low) 3.4905
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2611
    R-Factor(R-Work) 0.1932
    R-Factor(R-Free) 0.3221
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4905
    Shell Resolution(Low) 3.6744
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2575
    R-Factor(R-Work) 0.178
    R-Factor(R-Free) 0.2352
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6744
    Shell Resolution(Low) 3.9045
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2598
    R-Factor(R-Work) 0.1746
    R-Factor(R-Free) 0.24
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9045
    Shell Resolution(Low) 4.2058
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2602
    R-Factor(R-Work) 0.1705
    R-Factor(R-Free) 0.2113
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2058
    Shell Resolution(Low) 4.6287
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.1602
    R-Factor(R-Free) 0.2187
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6287
    Shell Resolution(Low) 5.2977
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2640
    R-Factor(R-Work) 0.1805
    R-Factor(R-Free) 0.2232
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2977
    Shell Resolution(Low) 6.6713
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2706
    R-Factor(R-Work) 0.2138
    R-Factor(R-Free) 0.2415
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6713
    Shell Resolution(Low) 46.235
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2729
    R-Factor(R-Work) 0.2257
    R-Factor(R-Free) 0.2653
    Percent Reflections(Observed) 96.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 16.117
    f_plane_restr 0.005
    f_chiral_restr 0.067
    f_angle_d 1.074
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7209
    Nucleic Acid Atoms 0
    Heterogen Atoms 100
    Solvent Atoms 86
     
     
  •   Software and Computing Hide
    Computing
    Data Collection UNKNOWN
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution BALBES
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALA version: 3.3.20