POP-OUT | CLOSE

An Information Portal to 108957 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4DVF
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 293.0
    Details 1.7M Li2SO4, 100mM HEPES, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 59.57 α = 90
    b = 85.82 β = 90
    c = 176.65 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 ADSC QUANTUM 315
    Collection Date 2012-02-17
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRF BEAMLINE BL17U
    Wavelength List 0.97915
    Site SSRF
    Beamline BL17U
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.8
    Resolution(Low) 35.48
    Number Reflections(All) 84247
    Number Reflections(Observed) 76885
    B(Isotropic) From Wilson Plot 23.64
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.803
    Resolution(Low) 35.477
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 84247
    Number of Reflections(Observed) 76885
    Number of Reflections(R-Free) 3836
    Percent Reflections(Observed) 91.18
    R-Factor(Observed) 0.2085
    R-Work 0.2069
    R-Free 0.2384
     
    Temperature Factor Modeling
    Mean Isotropic B Value 31.2088
    Anisotropic B[1][1] -2.3168
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 6.3537
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -4.0369
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8031
    Shell Resolution(Low) 1.8259
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2365
    R-Factor(R-Work) 0.2552
    R-Factor(R-Free) 0.3207
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8259
    Shell Resolution(Low) 1.8499
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2488
    R-Factor(R-Work) 0.2519
    R-Factor(R-Free) 0.2853
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8499
    Shell Resolution(Low) 1.8753
    Number of Reflections(R-Free) 108
    Number of Reflections(R-Work) 2460
    R-Factor(R-Work) 0.2651
    R-Factor(R-Free) 0.3299
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8753
    Shell Resolution(Low) 1.9021
    Number of Reflections(R-Free) 96
    Number of Reflections(R-Work) 1705
    R-Factor(R-Work) 0.2947
    R-Factor(R-Free) 0.3496
    Percent Reflections(Observed) 58.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9021
    Shell Resolution(Low) 1.9305
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2564
    R-Factor(R-Work) 0.4375
    R-Factor(R-Free) 0.4905
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9305
    Shell Resolution(Low) 1.9606
    Number of Reflections(R-Free) 82
    Number of Reflections(R-Work) 1901
    R-Factor(R-Work) 0.2675
    R-Factor(R-Free) 0.2326
    Percent Reflections(Observed) 64.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9606
    Shell Resolution(Low) 1.9928
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2556
    R-Factor(R-Work) 0.2376
    R-Factor(R-Free) 0.2823
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9928
    Shell Resolution(Low) 2.0271
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2730
    R-Factor(R-Work) 0.2289
    R-Factor(R-Free) 0.283
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0271
    Shell Resolution(Low) 2.064
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2758
    R-Factor(R-Work) 0.2159
    R-Factor(R-Free) 0.2746
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.064
    Shell Resolution(Low) 2.1037
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2730
    R-Factor(R-Work) 0.2257
    R-Factor(R-Free) 0.271
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1037
    Shell Resolution(Low) 2.1466
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2796
    R-Factor(R-Work) 0.2314
    R-Factor(R-Free) 0.2835
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1466
    Shell Resolution(Low) 2.1933
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2796
    R-Factor(R-Work) 0.2331
    R-Factor(R-Free) 0.2523
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1933
    Shell Resolution(Low) 2.2443
    Number of Reflections(R-Free) 113
    Number of Reflections(R-Work) 2395
    R-Factor(R-Work) 0.2565
    R-Factor(R-Free) 0.3367
    Percent Reflections(Observed) 82.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2443
    Shell Resolution(Low) 2.3004
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2518
    R-Factor(R-Work) 0.277
    R-Factor(R-Free) 0.3178
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3004
    Shell Resolution(Low) 2.3626
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2800
    R-Factor(R-Work) 0.2132
    R-Factor(R-Free) 0.2809
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3626
    Shell Resolution(Low) 2.4321
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 2810
    R-Factor(R-Work) 0.22
    R-Factor(R-Free) 0.2614
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4321
    Shell Resolution(Low) 2.5106
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 2887
    R-Factor(R-Work) 0.2196
    R-Factor(R-Free) 0.2394
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5106
    Shell Resolution(Low) 2.6003
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2936
    R-Factor(R-Work) 0.2111
    R-Factor(R-Free) 0.2641
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6003
    Shell Resolution(Low) 2.7043
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2936
    R-Factor(R-Work) 0.2185
    R-Factor(R-Free) 0.2565
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7043
    Shell Resolution(Low) 2.8274
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2961
    R-Factor(R-Work) 0.2148
    R-Factor(R-Free) 0.2672
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8274
    Shell Resolution(Low) 2.9764
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 2978
    R-Factor(R-Work) 0.2109
    R-Factor(R-Free) 0.2481
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9764
    Shell Resolution(Low) 3.1627
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2957
    R-Factor(R-Work) 0.1986
    R-Factor(R-Free) 0.2061
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1627
    Shell Resolution(Low) 3.4068
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2965
    R-Factor(R-Work) 0.1942
    R-Factor(R-Free) 0.2375
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4068
    Shell Resolution(Low) 3.7493
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2848
    R-Factor(R-Work) 0.1749
    R-Factor(R-Free) 0.1797
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7493
    Shell Resolution(Low) 4.291
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 3009
    R-Factor(R-Work) 0.154
    R-Factor(R-Free) 0.1868
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.291
    Shell Resolution(Low) 5.4031
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 3080
    R-Factor(R-Work) 0.1552
    R-Factor(R-Free) 0.1691
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4031
    Shell Resolution(Low) 35.4836
    Number of Reflections(R-Free) 192
    Number of Reflections(R-Work) 3120
    R-Factor(R-Work) 0.2127
    R-Factor(R-Free) 0.2236
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.233
    f_plane_restr 0.004
    f_chiral_restr 0.075
    f_angle_d 1.114
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5963
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 532
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    molecular replacement Phaser version: 2.1.4
    data reduction SCALA