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X-RAY DIFFRACTION
Materials and Methods page
4GPR
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 291.0
    Details EhUbc5 at 8 mg/mL concentration in buffer containing 50 mM HEPES and 100 mM NaCl was mixed 1:1 and equilibrated against crystallization solution (100 mM Tris, 14% (w/v) polyvinylpyrrolidone K 15, and 0.5 mM cobalt (II) chloride), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 46.97 α = 90
    b = 49.58 β = 90
    c = 63.46 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 MAR scanner 300 mm plate
    Collection Date 2012-07-16
     
    Diffraction Radiation
    Monochromator double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 22-BM
    Wavelength List 1.000
    Site APS
    Beamline 22-BM
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.34
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.6
    Resolution(Low) 50
    Number Reflections(All) 20139
    Number Reflections(Observed) 19998
    Percent Possible(Observed) 99.3
    R Merge I(Observed) 0.044
    B(Isotropic) From Wilson Plot 14.9
    Redundancy 8.2
     
    High Resolution Shell Details
    Resolution(High) 1.6
    Resolution(Low) 1.61
    Percent Possible(All) 87.3
    R Merge I(Observed) 0.309
    Mean I Over Sigma(Observed) 2.8
    Redundancy 3.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.6
    Resolution(Low) 39.069
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 20111
    Number of Reflections(Observed) 19950
    Number of Reflections(R-Free) 1998
    Percent Reflections(Observed) 99.2
    R-Factor(Observed) 0.1737
    R-Work 0.1706
    R-Free 0.2022
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6
    Shell Resolution(Low) 1.6417
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1148
    R-Factor(R-Work) 0.2057
    R-Factor(R-Free) 0.2595
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6417
    Shell Resolution(Low) 1.686
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1243
    R-Factor(R-Work) 0.1966
    R-Factor(R-Free) 0.2484
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.686
    Shell Resolution(Low) 1.7357
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1264
    R-Factor(R-Work) 0.1833
    R-Factor(R-Free) 0.2134
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7357
    Shell Resolution(Low) 1.7917
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 1282
    R-Factor(R-Work) 0.1904
    R-Factor(R-Free) 0.2243
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7917
    Shell Resolution(Low) 1.8557
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 1263
    R-Factor(R-Work) 0.1809
    R-Factor(R-Free) 0.2508
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8557
    Shell Resolution(Low) 1.93
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1294
    R-Factor(R-Work) 0.1792
    R-Factor(R-Free) 0.2453
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.93
    Shell Resolution(Low) 2.0178
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1273
    R-Factor(R-Work) 0.1756
    R-Factor(R-Free) 0.2112
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0178
    Shell Resolution(Low) 2.1242
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1284
    R-Factor(R-Work) 0.1612
    R-Factor(R-Free) 0.2134
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1242
    Shell Resolution(Low) 2.2573
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 1286
    R-Factor(R-Work) 0.1691
    R-Factor(R-Free) 0.1966
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2573
    Shell Resolution(Low) 2.4316
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1288
    R-Factor(R-Work) 0.1671
    R-Factor(R-Free) 0.204
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4316
    Shell Resolution(Low) 2.6762
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1291
    R-Factor(R-Work) 0.1813
    R-Factor(R-Free) 0.205
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6762
    Shell Resolution(Low) 3.0633
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 1308
    R-Factor(R-Work) 0.1748
    R-Factor(R-Free) 0.2122
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0633
    Shell Resolution(Low) 3.8589
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1330
    R-Factor(R-Work) 0.1651
    R-Factor(R-Free) 0.1939
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8589
    Shell Resolution(Low) 39.0808
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 1398
    R-Factor(R-Work) 0.1584
    R-Factor(R-Free) 0.1692
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.009
    f_chiral_restr 0.099
    f_dihedral_angle_d 13.0
    f_angle_d 1.504
    f_bond_d 0.014
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1195
    Nucleic Acid Atoms 0
    Heterogen Atoms 1
    Solvent Atoms 179
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX AutoMR
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8_1069)
    model building PHENIX version: AutoMR
    data collection HKL-2000