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X-RAY DIFFRACTION
Materials and Methods page
4IZG
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7
    Temperature 298.0
    Details Protein (10 mM Hepes pH 7.8, 150 mM NaCl, 5% glycerol, 1 mM EDTA/DTT); Reservoir (30% Peg300, MES pH 7.0, 200 mM MgCl); Cryoprotection (Reservoir+250 mM trans-4OH-L-Proline Betaine, comes with approx equal molar of iodine during synthesis of trans-4OH-L-Proline Betaine), temperature 298K, VAPOR DIFFUSION, SITTING DROP
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 117.46 α = 90
    b = 117.46 β = 90
    c = 111.05 γ = 90
     
    Space Group
    Space Group Name:    P 4 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX225HE
    Details MIRRORS
    Collection Date 2012-07-09
     
    Diffraction Radiation
    Monochromator GRAPHITE
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 31-ID
    Wavelength List 0.9793
    Site APS
    Beamline 31-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.7
    Resolution(Low) 111.05
    Number Reflections(All) 85566
    Number Reflections(Observed) 85566
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.104
    Redundancy 11.8
     
    High Resolution Shell Details
    Resolution(High) 1.7
    Resolution(Low) 1.79
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.773
    Mean I Over Sigma(Observed) 1.0
    R-Sym I(Observed) 0.773
    Redundancy 8.3
    Number Unique Reflections(All) 12278
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 1.7
    Resolution(Low) 80.696
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 85473
    Number of Reflections(Observed) 85473
    Number of Reflections(R-Free) 4275
    Percent Reflections(Observed) 99.82
    R-Factor(All) 0.1668
    R-Factor(Observed) 0.1668
    R-Work 0.1653
    R-Free 0.1966
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 16.388
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7
    Shell Resolution(Low) 1.7193
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2665
    R-Factor(R-Work) 0.2408
    R-Factor(R-Free) 0.3164
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7193
    Shell Resolution(Low) 1.7396
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 2687
    R-Factor(R-Work) 0.2231
    R-Factor(R-Free) 0.2707
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7396
    Shell Resolution(Low) 1.7608
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2659
    R-Factor(R-Work) 0.2136
    R-Factor(R-Free) 0.2469
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7608
    Shell Resolution(Low) 1.7831
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2674
    R-Factor(R-Work) 0.2101
    R-Factor(R-Free) 0.2412
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7831
    Shell Resolution(Low) 1.8065
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2672
    R-Factor(R-Work) 0.1986
    R-Factor(R-Free) 0.2232
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8065
    Shell Resolution(Low) 1.8313
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.187
    R-Factor(R-Free) 0.2197
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8313
    Shell Resolution(Low) 1.8574
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.188
    R-Factor(R-Free) 0.2626
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8574
    Shell Resolution(Low) 1.8852
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2669
    R-Factor(R-Work) 0.1847
    R-Factor(R-Free) 0.2188
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8852
    Shell Resolution(Low) 1.9146
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 2685
    R-Factor(R-Work) 0.18
    R-Factor(R-Free) 0.2112
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9146
    Shell Resolution(Low) 1.946
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2694
    R-Factor(R-Work) 0.1765
    R-Factor(R-Free) 0.2447
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.946
    Shell Resolution(Low) 1.9796
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.1789
    R-Factor(R-Free) 0.2094
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9796
    Shell Resolution(Low) 2.0156
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2654
    R-Factor(R-Work) 0.1682
    R-Factor(R-Free) 0.2074
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0156
    Shell Resolution(Low) 2.0544
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 2670
    R-Factor(R-Work) 0.166
    R-Factor(R-Free) 0.2136
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0544
    Shell Resolution(Low) 2.0963
    Number of Reflections(R-Free) 121
    Number of Reflections(R-Work) 2722
    R-Factor(R-Work) 0.1607
    R-Factor(R-Free) 0.2113
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0963
    Shell Resolution(Low) 2.1419
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.1667
    R-Factor(R-Free) 0.2037
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1419
    Shell Resolution(Low) 2.1917
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2683
    R-Factor(R-Work) 0.1525
    R-Factor(R-Free) 0.1891
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1917
    Shell Resolution(Low) 2.2465
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2679
    R-Factor(R-Work) 0.158
    R-Factor(R-Free) 0.2153
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2465
    Shell Resolution(Low) 2.3073
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2707
    R-Factor(R-Work) 0.1546
    R-Factor(R-Free) 0.1952
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3073
    Shell Resolution(Low) 2.3752
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2695
    R-Factor(R-Work) 0.1545
    R-Factor(R-Free) 0.196
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3752
    Shell Resolution(Low) 2.4518
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2697
    R-Factor(R-Work) 0.1626
    R-Factor(R-Free) 0.1967
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4518
    Shell Resolution(Low) 2.5395
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2693
    R-Factor(R-Work) 0.165
    R-Factor(R-Free) 0.1946
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5395
    Shell Resolution(Low) 2.6411
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2728
    R-Factor(R-Work) 0.1557
    R-Factor(R-Free) 0.1762
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6411
    Shell Resolution(Low) 2.7613
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2699
    R-Factor(R-Work) 0.1678
    R-Factor(R-Free) 0.1977
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7613
    Shell Resolution(Low) 2.9069
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 2706
    R-Factor(R-Work) 0.1699
    R-Factor(R-Free) 0.2228
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9069
    Shell Resolution(Low) 3.0891
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2756
    R-Factor(R-Work) 0.1673
    R-Factor(R-Free) 0.1859
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0891
    Shell Resolution(Low) 3.3276
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2740
    R-Factor(R-Work) 0.1533
    R-Factor(R-Free) 0.1864
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3276
    Shell Resolution(Low) 3.6625
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2757
    R-Factor(R-Work) 0.1487
    R-Factor(R-Free) 0.164
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6625
    Shell Resolution(Low) 4.1924
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2787
    R-Factor(R-Work) 0.1414
    R-Factor(R-Free) 0.1587
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1924
    Shell Resolution(Low) 5.2819
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2813
    R-Factor(R-Work) 0.1446
    R-Factor(R-Free) 0.1521
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2819
    Shell Resolution(Low) 80.7868
    Number of Reflections(R-Free) 171
    Number of Reflections(R-Work) 2947
    R-Factor(R-Work) 0.1837
    R-Factor(R-Free) 0.201
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.033
    f_plane_restr 0.006
    f_chiral_restr 0.068
    f_angle_d 1.103
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5538
    Nucleic Acid Atoms 0
    Heterogen Atoms 54
    Solvent Atoms 787
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALA version: 3.3.20