POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
4HD4
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 6.5
    Temperature 293.0
    Details PEG 8000, sodium cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 48 α = 90
    b = 78.58 β = 106.13
    c = 85.89 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Detector
    Collection Date 2011-02-17
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID23-1
    Wavelength List 0.976300
    Site ESRF
    Beamline ID23-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.8
    Resolution(Low) 36.53
    Number Reflections(All) 54388
    Number Reflections(Observed) 54388
    Percent Possible(Observed) 96.3
    R Merge I(Observed) 0.099
    Redundancy 3.3
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.9
    Percent Possible(All) 96.3
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 28.451
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 54339
    Number of Reflections(R-Free) 5457
    Percent Reflections(Observed) 95.62
    R-Factor(Observed) 0.2088
    R-Work 0.2066
    R-Free 0.2284
     
    Temperature Factor Modeling
    Anisotropic B[1][1] 0.3479
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.4876
    Anisotropic B[2][2] -3.75
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.3924
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.8205
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 1636
    R-Factor(R-Work) 0.2276
    R-Factor(R-Free) 0.2835
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8205
    Shell Resolution(Low) 1.8419
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 1631
    R-Factor(R-Work) 0.2155
    R-Factor(R-Free) 0.2511
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8419
    Shell Resolution(Low) 1.8643
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 1624
    R-Factor(R-Work) 0.2187
    R-Factor(R-Free) 0.2423
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8643
    Shell Resolution(Low) 1.8879
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 1622
    R-Factor(R-Work) 0.2158
    R-Factor(R-Free) 0.2485
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8879
    Shell Resolution(Low) 1.9128
    Number of Reflections(R-Free) 192
    Number of Reflections(R-Work) 1676
    R-Factor(R-Work) 0.2251
    R-Factor(R-Free) 0.255
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9128
    Shell Resolution(Low) 1.939
    Number of Reflections(R-Free) 193
    Number of Reflections(R-Work) 1579
    R-Factor(R-Work) 0.2095
    R-Factor(R-Free) 0.2643
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.939
    Shell Resolution(Low) 1.9667
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 1640
    R-Factor(R-Work) 0.2125
    R-Factor(R-Free) 0.2799
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9667
    Shell Resolution(Low) 1.996
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 1659
    R-Factor(R-Work) 0.2158
    R-Factor(R-Free) 0.2554
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.996
    Shell Resolution(Low) 2.0272
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 1571
    R-Factor(R-Work) 0.2322
    R-Factor(R-Free) 0.2431
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0272
    Shell Resolution(Low) 2.0604
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 1654
    R-Factor(R-Work) 0.2214
    R-Factor(R-Free) 0.2594
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0604
    Shell Resolution(Low) 2.0959
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 1665
    R-Factor(R-Work) 0.2325
    R-Factor(R-Free) 0.2692
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0959
    Shell Resolution(Low) 2.134
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 1617
    R-Factor(R-Work) 0.2218
    R-Factor(R-Free) 0.2452
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.134
    Shell Resolution(Low) 2.1751
    Number of Reflections(R-Free) 180
    Number of Reflections(R-Work) 1690
    R-Factor(R-Work) 0.218
    R-Factor(R-Free) 0.2345
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1751
    Shell Resolution(Low) 2.2195
    Number of Reflections(R-Free) 196
    Number of Reflections(R-Work) 1595
    R-Factor(R-Work) 0.2097
    R-Factor(R-Free) 0.2293
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2195
    Shell Resolution(Low) 2.2677
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 1670
    R-Factor(R-Work) 0.2053
    R-Factor(R-Free) 0.2416
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2677
    Shell Resolution(Low) 2.3204
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 1648
    R-Factor(R-Work) 0.2151
    R-Factor(R-Free) 0.233
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3204
    Shell Resolution(Low) 2.3784
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 1669
    R-Factor(R-Work) 0.2102
    R-Factor(R-Free) 0.2168
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3784
    Shell Resolution(Low) 2.4427
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 1621
    R-Factor(R-Work) 0.2119
    R-Factor(R-Free) 0.2377
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4427
    Shell Resolution(Low) 2.5145
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 1645
    R-Factor(R-Work) 0.2179
    R-Factor(R-Free) 0.25
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5145
    Shell Resolution(Low) 2.5956
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 1652
    R-Factor(R-Work) 0.2196
    R-Factor(R-Free) 0.2656
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5956
    Shell Resolution(Low) 2.6884
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 1667
    R-Factor(R-Work) 0.2191
    R-Factor(R-Free) 0.248
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6884
    Shell Resolution(Low) 2.7959
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 1649
    R-Factor(R-Work) 0.2274
    R-Factor(R-Free) 0.2335
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7959
    Shell Resolution(Low) 2.923
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 1647
    R-Factor(R-Work) 0.2116
    R-Factor(R-Free) 0.2087
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.923
    Shell Resolution(Low) 3.077
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 1655
    R-Factor(R-Work) 0.213
    R-Factor(R-Free) 0.2417
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.077
    Shell Resolution(Low) 3.2695
    Number of Reflections(R-Free) 196
    Number of Reflections(R-Work) 1618
    R-Factor(R-Work) 0.2182
    R-Factor(R-Free) 0.2338
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2695
    Shell Resolution(Low) 3.5215
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 1604
    R-Factor(R-Work) 0.211
    R-Factor(R-Free) 0.233
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5215
    Shell Resolution(Low) 3.8751
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 1622
    R-Factor(R-Work) 0.1862
    R-Factor(R-Free) 0.2096
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8751
    Shell Resolution(Low) 4.434
    Number of Reflections(R-Free) 176
    Number of Reflections(R-Work) 1605
    R-Factor(R-Work) 0.1631
    R-Factor(R-Free) 0.1835
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.434
    Shell Resolution(Low) 5.5795
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 1596
    R-Factor(R-Work) 0.1647
    R-Factor(R-Free) 0.1587
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5795
    Shell Resolution(Low) 28.4549
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 1455
    R-Factor(R-Work) 0.1879
    R-Factor(R-Free) 0.1797
    Percent Reflections(Observed) 82.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.096
    f_dihedral_angle_d 16.135
    f_angle_d 1.222
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4708
    Nucleic Acid Atoms 0
    Heterogen Atoms 2
    Solvent Atoms 236
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction SCALA
    data collection Mosflm