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X-RAY DIFFRACTION
Materials and Methods page
4J9T
  •   Crystallization Hide
    Crystallization Experiments
    Method Microbatch under oil
    pH 6.5
    Temperature 277.0
    Details protein buffer: 10 mM Tris HCl (pH 8). Precipitation cocktail: 100 MM NA CACODYLATE (PH 6.5), 5 mM FeCl2, 15% PEG 3350 Microbatch under oil, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 46.16 α = 90
    b = 79.68 β = 90
    c = 83.78 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 CCD 165 mm
    Details mirrors
    Collection Date 2012-10-12
     
    Diffraction Radiation
    Monochromator Si 111 CHANNEL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X4C
    Wavelength List 0.97012
    Site NSLS
    Beamline X4C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.4
    Resolution(Low) 31.02
    Number Reflections(Observed) 61532
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.059
    B(Isotropic) From Wilson Plot 11.2
    Redundancy 6.1
     
    High Resolution Shell Details
    Resolution(High) 1.4
    Resolution(Low) 1.45
    Percent Possible(All) 99.7
    R Merge I(Observed) 0.42
    Mean I Over Sigma(Observed) 4.9
    R-Sym I(Observed) 0.405
    Redundancy 4.9
    Number Unique Reflections(All) 6060
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.4
    Resolution(Low) 31.021
    Cut-off Sigma(I) 1.3
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 61546
    Number of Reflections(Observed) 61460
    Number of Reflections(R-Free) 6183
    Percent Reflections(Observed) 99.86
    R-Factor(All) 0.1394
    R-Factor(Observed) 0.1382
    R-Work 0.1349
    R-Free 0.1662
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Anisotropic B[1][1] -1.2254
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.8007
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.4246
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4003
    Shell Resolution(Low) 1.4162
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 1769
    R-Factor(R-Work) 0.2995
    R-Factor(R-Free) 0.3782
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4162
    Shell Resolution(Low) 1.4328
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 1808
    R-Factor(R-Work) 0.247
    R-Factor(R-Free) 0.2684
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4328
    Shell Resolution(Low) 1.4503
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 1820
    R-Factor(R-Work) 0.2149
    R-Factor(R-Free) 0.2578
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4503
    Shell Resolution(Low) 1.4687
    Number of Reflections(R-Free) 193
    Number of Reflections(R-Work) 1813
    R-Factor(R-Work) 0.1738
    R-Factor(R-Free) 0.1927
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4687
    Shell Resolution(Low) 1.488
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 1827
    R-Factor(R-Work) 0.1662
    R-Factor(R-Free) 0.22
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.488
    Shell Resolution(Low) 1.5084
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 1799
    R-Factor(R-Work) 0.1509
    R-Factor(R-Free) 0.2006
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5084
    Shell Resolution(Low) 1.5299
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 1800
    R-Factor(R-Work) 0.1451
    R-Factor(R-Free) 0.1949
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5299
    Shell Resolution(Low) 1.5528
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 1852
    R-Factor(R-Work) 0.127
    R-Factor(R-Free) 0.1965
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5528
    Shell Resolution(Low) 1.577
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 1831
    R-Factor(R-Work) 0.1196
    R-Factor(R-Free) 0.1849
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.577
    Shell Resolution(Low) 1.6029
    Number of Reflections(R-Free) 201
    Number of Reflections(R-Work) 1832
    R-Factor(R-Work) 0.1158
    R-Factor(R-Free) 0.1761
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6029
    Shell Resolution(Low) 1.6305
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 1831
    R-Factor(R-Work) 0.1119
    R-Factor(R-Free) 0.176
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6305
    Shell Resolution(Low) 1.6602
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 1841
    R-Factor(R-Work) 0.1053
    R-Factor(R-Free) 0.1594
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6602
    Shell Resolution(Low) 1.6921
    Number of Reflections(R-Free) 191
    Number of Reflections(R-Work) 1820
    R-Factor(R-Work) 0.1064
    R-Factor(R-Free) 0.1485
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6921
    Shell Resolution(Low) 1.7266
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 1824
    R-Factor(R-Work) 0.1087
    R-Factor(R-Free) 0.1667
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7266
    Shell Resolution(Low) 1.7642
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 1815
    R-Factor(R-Work) 0.1009
    R-Factor(R-Free) 0.1529
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7642
    Shell Resolution(Low) 1.8052
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 1861
    R-Factor(R-Work) 0.1024
    R-Factor(R-Free) 0.1566
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8052
    Shell Resolution(Low) 1.8503
    Number of Reflections(R-Free) 201
    Number of Reflections(R-Work) 1825
    R-Factor(R-Work) 0.1057
    R-Factor(R-Free) 0.1529
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8503
    Shell Resolution(Low) 1.9004
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 1824
    R-Factor(R-Work) 0.1163
    R-Factor(R-Free) 0.1458
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9004
    Shell Resolution(Low) 1.9563
    Number of Reflections(R-Free) 214
    Number of Reflections(R-Work) 1831
    R-Factor(R-Work) 0.1185
    R-Factor(R-Free) 0.166
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9563
    Shell Resolution(Low) 2.0194
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 1824
    R-Factor(R-Work) 0.123
    R-Factor(R-Free) 0.1618
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0194
    Shell Resolution(Low) 2.0916
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 1884
    R-Factor(R-Work) 0.1238
    R-Factor(R-Free) 0.1572
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0916
    Shell Resolution(Low) 2.1753
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 1850
    R-Factor(R-Work) 0.1263
    R-Factor(R-Free) 0.1547
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1753
    Shell Resolution(Low) 2.2743
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 1874
    R-Factor(R-Work) 0.1231
    R-Factor(R-Free) 0.155
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2743
    Shell Resolution(Low) 2.3941
    Number of Reflections(R-Free) 216
    Number of Reflections(R-Work) 1839
    R-Factor(R-Work) 0.13
    R-Factor(R-Free) 0.1599
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3941
    Shell Resolution(Low) 2.5441
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 1873
    R-Factor(R-Work) 0.1331
    R-Factor(R-Free) 0.1651
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5441
    Shell Resolution(Low) 2.7404
    Number of Reflections(R-Free) 214
    Number of Reflections(R-Work) 1849
    R-Factor(R-Work) 0.1343
    R-Factor(R-Free) 0.1642
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7404
    Shell Resolution(Low) 3.0159
    Number of Reflections(R-Free) 204
    Number of Reflections(R-Work) 1873
    R-Factor(R-Work) 0.1401
    R-Factor(R-Free) 0.1622
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0159
    Shell Resolution(Low) 3.4519
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 1890
    R-Factor(R-Work) 0.1372
    R-Factor(R-Free) 0.1501
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4519
    Shell Resolution(Low) 4.3471
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 1913
    R-Factor(R-Work) 0.131
    R-Factor(R-Free) 0.1447
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3471
    Shell Resolution(Low) 31.0286
    Number of Reflections(R-Free) 235
    Number of Reflections(R-Work) 1985
    R-Factor(R-Work) 0.171
    R-Factor(R-Free) 0.1719
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.069
    f_dihedral_angle_d 12.698
    f_angle_d 1.148
    f_bond_d 0.007
     
    Coordinate Error
    Luzzati ESD(Observed) 0.13
    Luzzati Sigma A(Observed) 0.09
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.13
    Luzzati Sigma A(R-Free Set) 0.09
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2675
    Nucleic Acid Atoms 0
    Heterogen Atoms 7
    Solvent Atoms 527
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution COMO
    Structure Refinement PHENIX (phenix.refine: 1.7_650)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7_650)
    refinement CNS1.3
    refinement XtalView
    model building COMO
    data collection ADSC version: Quantum