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X-RAY DIFFRACTION
Materials and Methods page
4GYP
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, sitting drop
    Temperature 282.0
    Details Protein solution was at 12.5 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME. Mother liqueur contained 0.17 M Ammonium acetate, 0.085 M Na-citrate tribasic, dihydrate (pH 5.6), 25.5% PEG 4,000 and 15% v/v glycerol, vapor diffusion, sitting drop, temperature 282K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 155.47 α = 90
    b = 113.02 β = 105.89
    c = 128.59 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type RAYONIX MX-300
    Collection Date 2012-02-15
     
    Diffraction Radiation
    Monochromator C(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-G
    Wavelength List 0.97857
    Site APS
    Beamline 21-ID-G
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.1
    Resolution(Low) 30
    Number Reflections(Observed) 118199
    Percent Possible(Observed) 99.5
    B(Isotropic) From Wilson Plot 23.762
     
    High Resolution Shell Details
    Resolution(High) 2.1
    Resolution(Low) 2.15
    Percent Possible(All) 99.8
    R Merge I(Observed) 0.609
    Mean I Over Sigma(Observed) 2.44
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.1
    Resolution(Low) 29.965
    Cut-off Sigma(F) 1.99
    Number of Reflections(Observed) 118199
    Number of Reflections(R-Free) 6221
    Percent Reflections(Observed) 99.91
    R-Factor(All) 0.172
    R-Factor(Observed) 0.1505
    R-Work 0.1486
    R-Free 0.1863
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 16.293
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1
    Shell Resolution(Low) 2.1239
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 3939
    R-Factor(R-Work) 0.1828
    R-Factor(R-Free) 0.2422
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1239
    Shell Resolution(Low) 2.1489
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3909
    R-Factor(R-Work) 0.1784
    R-Factor(R-Free) 0.2614
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1489
    Shell Resolution(Low) 2.1751
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 3930
    R-Factor(R-Work) 0.1732
    R-Factor(R-Free) 0.2252
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1751
    Shell Resolution(Low) 2.2026
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 3905
    R-Factor(R-Work) 0.1697
    R-Factor(R-Free) 0.2158
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2026
    Shell Resolution(Low) 2.2315
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 3950
    R-Factor(R-Work) 0.1691
    R-Factor(R-Free) 0.231
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2315
    Shell Resolution(Low) 2.2621
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 3928
    R-Factor(R-Work) 0.1704
    R-Factor(R-Free) 0.2355
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2621
    Shell Resolution(Low) 2.2944
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 3942
    R-Factor(R-Work) 0.1735
    R-Factor(R-Free) 0.2575
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2944
    Shell Resolution(Low) 2.3286
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 3897
    R-Factor(R-Work) 0.1699
    R-Factor(R-Free) 0.2385
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3286
    Shell Resolution(Low) 2.365
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3919
    R-Factor(R-Work) 0.1645
    R-Factor(R-Free) 0.2266
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.365
    Shell Resolution(Low) 2.4038
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 3960
    R-Factor(R-Work) 0.1582
    R-Factor(R-Free) 0.228
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4038
    Shell Resolution(Low) 2.4452
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3911
    R-Factor(R-Work) 0.1642
    R-Factor(R-Free) 0.2259
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4452
    Shell Resolution(Low) 2.4897
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3906
    R-Factor(R-Work) 0.1592
    R-Factor(R-Free) 0.2095
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4897
    Shell Resolution(Low) 2.5375
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 3947
    R-Factor(R-Work) 0.1565
    R-Factor(R-Free) 0.2004
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5375
    Shell Resolution(Low) 2.5893
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 3953
    R-Factor(R-Work) 0.1529
    R-Factor(R-Free) 0.2089
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5893
    Shell Resolution(Low) 2.6456
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 3904
    R-Factor(R-Work) 0.1496
    R-Factor(R-Free) 0.2091
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6456
    Shell Resolution(Low) 2.7071
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 3895
    R-Factor(R-Work) 0.1557
    R-Factor(R-Free) 0.2086
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7071
    Shell Resolution(Low) 2.7747
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 3940
    R-Factor(R-Work) 0.1533
    R-Factor(R-Free) 0.2054
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7747
    Shell Resolution(Low) 2.8497
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 3947
    R-Factor(R-Work) 0.1498
    R-Factor(R-Free) 0.1878
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8497
    Shell Resolution(Low) 2.9335
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3918
    R-Factor(R-Work) 0.1487
    R-Factor(R-Free) 0.1908
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9335
    Shell Resolution(Low) 3.0281
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 3941
    R-Factor(R-Work) 0.1538
    R-Factor(R-Free) 0.2097
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0281
    Shell Resolution(Low) 3.1362
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 3943
    R-Factor(R-Work) 0.1497
    R-Factor(R-Free) 0.1773
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1362
    Shell Resolution(Low) 3.2616
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 3927
    R-Factor(R-Work) 0.1428
    R-Factor(R-Free) 0.1957
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2616
    Shell Resolution(Low) 3.4098
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 3958
    R-Factor(R-Work) 0.136
    R-Factor(R-Free) 0.1635
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4098
    Shell Resolution(Low) 3.5893
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 3955
    R-Factor(R-Work) 0.1334
    R-Factor(R-Free) 0.1549
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5893
    Shell Resolution(Low) 3.8138
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 3954
    R-Factor(R-Work) 0.1245
    R-Factor(R-Free) 0.1508
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8138
    Shell Resolution(Low) 4.1076
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 3949
    R-Factor(R-Work) 0.1205
    R-Factor(R-Free) 0.1552
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1076
    Shell Resolution(Low) 4.5197
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 3973
    R-Factor(R-Work) 0.1245
    R-Factor(R-Free) 0.1512
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5197
    Shell Resolution(Low) 5.1708
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 3971
    R-Factor(R-Work) 0.1305
    R-Factor(R-Free) 0.1219
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1708
    Shell Resolution(Low) 6.5037
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 3989
    R-Factor(R-Work) 0.1587
    R-Factor(R-Free) 0.1579
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5037
    Shell Resolution(Low) 29.9678
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 4043
    R-Factor(R-Work) 0.1573
    R-Factor(R-Free) 0.1638
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.003
    f_plane_restr 0.005
    f_chiral_restr 0.072
    f_angle_d 1.029
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 13568
    Nucleic Acid Atoms 0
    Heterogen Atoms 102
    Solvent Atoms 1450
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8_1066)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction Xscale