POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
3VNR
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7.2
    Temperature 293.0
    Details 0.1M ammonium sulfate, 24-32% PEG5000 monomethyl ether, 1mM ATP, 100mM Hepes buffer, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 157.02 α = 90
    b = 157.02 β = 90
    c = 157.02 γ = 90
     
    Space Group
    Space Group Name:    I 2 3
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210
    Details mirrors
    Collection Date 2006-12-14
     
    Diffraction Radiation
    Monochromator Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL44B2
    Wavelength List 1.0
    Site SPRING-8
    Beamline BL44B2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.75
    Resolution(Low) 50
    Number Reflections(Observed) 64664
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.046
    Redundancy 16.8
     
    High Resolution Shell Details
    Resolution(High) 1.75
    Resolution(Low) 1.78
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.474
    Mean I Over Sigma(Observed) 6.643
    R-Sym I(Observed) 0.474
    Redundancy 16.8
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.75
    Resolution(Low) 35.11
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 64597
    Number of Reflections(R-Free) 3256
    Percent Reflections(Observed) 99.92
    R-Factor(Observed) 0.1899
    R-Work 0.1888
    R-Free 0.211
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 26.7731
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.75
    Shell Resolution(Low) 1.7762
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.2202
    R-Factor(R-Free) 0.2683
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7762
    Shell Resolution(Low) 1.8039
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2651
    R-Factor(R-Work) 0.2197
    R-Factor(R-Free) 0.2521
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8039
    Shell Resolution(Low) 1.8335
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2713
    R-Factor(R-Work) 0.2169
    R-Factor(R-Free) 0.2556
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8335
    Shell Resolution(Low) 1.8651
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2623
    R-Factor(R-Work) 0.2185
    R-Factor(R-Free) 0.2728
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8651
    Shell Resolution(Low) 1.899
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.2143
    R-Factor(R-Free) 0.271
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.899
    Shell Resolution(Low) 1.9355
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.1985
    R-Factor(R-Free) 0.2447
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9355
    Shell Resolution(Low) 1.975
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2660
    R-Factor(R-Work) 0.2092
    R-Factor(R-Free) 0.2403
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.975
    Shell Resolution(Low) 2.018
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.1922
    R-Factor(R-Free) 0.2247
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.018
    Shell Resolution(Low) 2.0649
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.1898
    R-Factor(R-Free) 0.1959
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0649
    Shell Resolution(Low) 2.1165
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 2647
    R-Factor(R-Work) 0.1831
    R-Factor(R-Free) 0.1884
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1165
    Shell Resolution(Low) 2.1738
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2642
    R-Factor(R-Work) 0.1942
    R-Factor(R-Free) 0.2279
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1738
    Shell Resolution(Low) 2.2377
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.1871
    R-Factor(R-Free) 0.2693
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2377
    Shell Resolution(Low) 2.3099
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.1905
    R-Factor(R-Free) 0.2027
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3099
    Shell Resolution(Low) 2.3925
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2660
    R-Factor(R-Work) 0.1927
    R-Factor(R-Free) 0.228
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3925
    Shell Resolution(Low) 2.4882
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.1922
    R-Factor(R-Free) 0.2238
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4882
    Shell Resolution(Low) 2.6014
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.1987
    R-Factor(R-Free) 0.238
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6014
    Shell Resolution(Low) 2.7385
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2666
    R-Factor(R-Work) 0.2
    R-Factor(R-Free) 0.214
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7385
    Shell Resolution(Low) 2.9101
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2676
    R-Factor(R-Work) 0.1949
    R-Factor(R-Free) 0.2275
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9101
    Shell Resolution(Low) 3.1346
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2697
    R-Factor(R-Work) 0.1973
    R-Factor(R-Free) 0.2122
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1346
    Shell Resolution(Low) 3.4498
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.1986
    R-Factor(R-Free) 0.2264
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4498
    Shell Resolution(Low) 3.9484
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2702
    R-Factor(R-Work) 0.1756
    R-Factor(R-Free) 0.1898
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9484
    Shell Resolution(Low) 4.9723
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2723
    R-Factor(R-Work) 0.1544
    R-Factor(R-Free) 0.143
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9723
    Shell Resolution(Low) 35.1169
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2742
    R-Factor(R-Work) 0.189
    R-Factor(R-Free) 0.209
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 12.669
    f_plane_restr 0.008
    f_chiral_restr 0.107
    f_angle_d 1.517
    f_bond_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3783
    Nucleic Acid Atoms 0
    Heterogen Atoms 30
    Solvent Atoms 315
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BSS
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution MOLREP
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    molecular replacement MOLREP
    data reduction HKL