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X-RAY DIFFRACTION
Materials and Methods page
4IVF
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, sitting drop
    pH 5.6
    Temperature 298.0
    Details Protein (10 mM Hepes pH 7.5, 100 mM NaCl); Reservoir (0.17M Amm Acetate, 0.085 M Sodium Citrate pH 5.6, 25.5% Peg4000, 15% (V/V) glycerol); Cryoprotection (Reservoir taken to 20% glycerol), vapor diffusion, sitting drop, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 90.6 α = 90
    b = 112.48 β = 90
    c = 194.38 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 RAYONIX MX225HE
    Details MIRRORS
    Collection Date 2012-10-16
     
    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) 2.2
    Resolution(Low) 194.38
    Number Reflections(All) 99618
    Number Reflections(Observed) 99618
    Percent Possible(Observed) 98.5
    Redundancy 6.1
     
    High Resolution Shell Details
    Resolution(High) 2.2
    Resolution(Low) 2.32
    Percent Possible(All) 97.9
    R Merge I(Observed) 0.7
    Mean I Over Sigma(Observed) 1.1
    R-Sym I(Observed) 0.7
    Redundancy 6.1
    Number Unique Reflections(All) 14286
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.2
    Resolution(Low) 37.126
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 99532
    Number of Reflections(Observed) 99532
    Number of Reflections(R-Free) 4984
    Percent Reflections(Observed) 98.2
    R-Factor(Observed) 0.1592
    R-Work 0.1559
    R-Free 0.2234
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 24.4895
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2
    Shell Resolution(Low) 2.225
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 3082
    R-Factor(R-Work) 0.2123
    R-Factor(R-Free) 0.3011
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.225
    Shell Resolution(Low) 2.2512
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 3111
    R-Factor(R-Work) 0.2256
    R-Factor(R-Free) 0.3067
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2512
    Shell Resolution(Low) 2.2786
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 3046
    R-Factor(R-Work) 0.2118
    R-Factor(R-Free) 0.2858
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2786
    Shell Resolution(Low) 2.3075
    Number of Reflections(R-Free) 179
    Number of Reflections(R-Work) 3107
    R-Factor(R-Work) 0.2021
    R-Factor(R-Free) 0.32
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3075
    Shell Resolution(Low) 2.3378
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 3091
    R-Factor(R-Work) 0.2041
    R-Factor(R-Free) 0.2714
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3378
    Shell Resolution(Low) 2.3698
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 3129
    R-Factor(R-Work) 0.1896
    R-Factor(R-Free) 0.2774
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3698
    Shell Resolution(Low) 2.4037
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 3086
    R-Factor(R-Work) 0.1975
    R-Factor(R-Free) 0.294
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4037
    Shell Resolution(Low) 2.4396
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3111
    R-Factor(R-Work) 0.205
    R-Factor(R-Free) 0.2752
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4396
    Shell Resolution(Low) 2.4777
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 3062
    R-Factor(R-Work) 0.1971
    R-Factor(R-Free) 0.2919
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4777
    Shell Resolution(Low) 2.5183
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 3139
    R-Factor(R-Work) 0.1963
    R-Factor(R-Free) 0.2939
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5183
    Shell Resolution(Low) 2.5617
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3088
    R-Factor(R-Work) 0.19
    R-Factor(R-Free) 0.2747
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5617
    Shell Resolution(Low) 2.6083
    Number of Reflections(R-Free) 183
    Number of Reflections(R-Work) 3116
    R-Factor(R-Work) 0.178
    R-Factor(R-Free) 0.2753
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6083
    Shell Resolution(Low) 2.6584
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 3110
    R-Factor(R-Work) 0.1768
    R-Factor(R-Free) 0.2612
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6584
    Shell Resolution(Low) 2.7127
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 3111
    R-Factor(R-Work) 0.169
    R-Factor(R-Free) 0.235
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7127
    Shell Resolution(Low) 2.7716
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 3147
    R-Factor(R-Work) 0.1657
    R-Factor(R-Free) 0.2833
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7716
    Shell Resolution(Low) 2.8361
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 3112
    R-Factor(R-Work) 0.1636
    R-Factor(R-Free) 0.255
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8361
    Shell Resolution(Low) 2.907
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 3128
    R-Factor(R-Work) 0.1633
    R-Factor(R-Free) 0.233
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.907
    Shell Resolution(Low) 2.9856
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 3156
    R-Factor(R-Work) 0.1644
    R-Factor(R-Free) 0.2767
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9856
    Shell Resolution(Low) 3.0734
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 3148
    R-Factor(R-Work) 0.1663
    R-Factor(R-Free) 0.2323
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0734
    Shell Resolution(Low) 3.1725
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 3145
    R-Factor(R-Work) 0.1613
    R-Factor(R-Free) 0.2537
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1725
    Shell Resolution(Low) 3.2858
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 3176
    R-Factor(R-Work) 0.1538
    R-Factor(R-Free) 0.2291
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2858
    Shell Resolution(Low) 3.4173
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3167
    R-Factor(R-Work) 0.1423
    R-Factor(R-Free) 0.2018
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4173
    Shell Resolution(Low) 3.5727
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 3122
    R-Factor(R-Work) 0.1294
    R-Factor(R-Free) 0.1732
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5727
    Shell Resolution(Low) 3.7609
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 3183
    R-Factor(R-Work) 0.1235
    R-Factor(R-Free) 0.1679
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7609
    Shell Resolution(Low) 3.9963
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3156
    R-Factor(R-Work) 0.1253
    R-Factor(R-Free) 0.1802
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9963
    Shell Resolution(Low) 4.3044
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 3241
    R-Factor(R-Work) 0.1227
    R-Factor(R-Free) 0.1777
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3044
    Shell Resolution(Low) 4.7368
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 3254
    R-Factor(R-Work) 0.1192
    R-Factor(R-Free) 0.1693
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7368
    Shell Resolution(Low) 5.4204
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 3272
    R-Factor(R-Work) 0.1235
    R-Factor(R-Free) 0.1732
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4204
    Shell Resolution(Low) 6.8222
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3346
    R-Factor(R-Work) 0.1494
    R-Factor(R-Free) 0.2269
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.8222
    Shell Resolution(Low) 37.1311
    Number of Reflections(R-Free) 192
    Number of Reflections(R-Work) 3406
    R-Factor(R-Work) 0.1619
    R-Factor(R-Free) 0.1777
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.636
    f_plane_restr 0.005
    f_chiral_restr 0.075
    f_angle_d 1.018
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 14481
    Nucleic Acid Atoms 0
    Heterogen Atoms 333
    Solvent Atoms 1271
     
     
  •   Software and Computing Hide
    Computing
    Data Collection UKNOWN
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution BALBES
    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
    data collection Mosflm