POP-OUT | CLOSE

An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DVG
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.5
    Temperature 293.0
    Details EhRho1-GTPgammaS at 5 mg/mL and and EhFormin1 at 10 mg/mL were mixed in crystallization buffer (50 mM Tris pH 8.0, 250 mM NaCl, 2.5% (v/v) glycerol, 5 mM DTT, 50 microM GTPgammaS, 1 mM magnesium chloride) and allowed to form a complex for 30 minutes at room temperature. The protein solution was then mixed 1:1 and equilibrated against crystallization solution (18% PEG 3350, 100 mM Tris pH 8.5, 200 mM magnesium chloride)., VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 138.56 α = 90
    b = 138.56 β = 90
    c = 57.76 γ = 120
     
    Space Group
    Space Group Name:    P 61
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MAR scanner 300 mm plate
    Collection Date 2011-11-22
     
    Diffraction Radiation
    Monochromator double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 23-ID-B
    Wavelength List 0.9795
    Site APS
    Beamline 23-ID-B
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.6
    Resolution(Low) 40
    Number Reflections(Observed) 19500
    Percent Possible(Observed) 98.4
    R Merge I(Observed) 0.085
    B(Isotropic) From Wilson Plot 65.0
    Redundancy 9.6
     
    High Resolution Shell Details
    Resolution(High) 2.6
    Resolution(Low) 2.63
    R Merge I(Observed) 0.58
    Mean I Over Sigma(Observed) 2.1
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.604
    Resolution(Low) 35.673
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 19211
    Number of Reflections(R-Free) 1938
    Percent Reflections(Observed) 97.85
    R-Factor(Observed) 0.2188
    R-Work 0.2152
    R-Free 0.2512
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -3.0438
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -3.0438
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 6.0876
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.604
    Shell Resolution(Low) 2.6687
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 1092
    R-Factor(R-Work) 0.3343
    R-Factor(R-Free) 0.3721
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6687
    Shell Resolution(Low) 2.7408
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1164
    R-Factor(R-Work) 0.3402
    R-Factor(R-Free) 0.366
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7408
    Shell Resolution(Low) 2.8215
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 1186
    R-Factor(R-Work) 0.3108
    R-Factor(R-Free) 0.3578
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8215
    Shell Resolution(Low) 2.9125
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1235
    R-Factor(R-Work) 0.2911
    R-Factor(R-Free) 0.3393
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9125
    Shell Resolution(Low) 3.0165
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 1232
    R-Factor(R-Work) 0.269
    R-Factor(R-Free) 0.3
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0165
    Shell Resolution(Low) 3.1372
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1230
    R-Factor(R-Work) 0.2473
    R-Factor(R-Free) 0.2896
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1372
    Shell Resolution(Low) 3.2799
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 1254
    R-Factor(R-Work) 0.2489
    R-Factor(R-Free) 0.3144
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2799
    Shell Resolution(Low) 3.4527
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1260
    R-Factor(R-Work) 0.248
    R-Factor(R-Free) 0.3285
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4527
    Shell Resolution(Low) 3.6688
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 1253
    R-Factor(R-Work) 0.234
    R-Factor(R-Free) 0.273
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6688
    Shell Resolution(Low) 3.9518
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1261
    R-Factor(R-Work) 0.2008
    R-Factor(R-Free) 0.2232
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9518
    Shell Resolution(Low) 4.3488
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1257
    R-Factor(R-Work) 0.1745
    R-Factor(R-Free) 0.2102
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3488
    Shell Resolution(Low) 4.9767
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 1275
    R-Factor(R-Work) 0.1573
    R-Factor(R-Free) 0.19
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9767
    Shell Resolution(Low) 6.2645
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 1278
    R-Factor(R-Work) 0.2088
    R-Factor(R-Free) 0.2112
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2645
    Shell Resolution(Low) 35.6767
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1296
    R-Factor(R-Work) 0.2027
    R-Factor(R-Free) 0.244
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.079
    f_dihedral_angle_d 14.668
    f_angle_d 1.233
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3747
    Nucleic Acid Atoms 0
    Heterogen Atoms 33
    Solvent Atoms 4
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX AutoSol
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.1_743)
    model building PHENIX version: AutoSol
    data collection HKL-2000