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X-RAY DIFFRACTION
Materials and Methods page
4IND
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 4.2
    Temperature 291.0
    Details 10 mg/mL Se-Met protein, 0.1 M sodium phosphate/citric acid, pH 4.2, 30-40% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 291K
    Method VAPOR DIFFUSION, SITTING DROP
    pH 4.2
    Temperature 291.0
    Details 10 mg/mL native protein, 0.1 M sodium phosphate/citric acid, pH 4.2, 30-40% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 81.77 α = 81.84
    b = 167 β = 82.17
    c = 186.98 γ = 81.44
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
    Diffrn ID 2
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 325 mm CCD
    Details Sample to detector distance: 100 to 650 mm, Maximum vertical offset: 200 mm
    Collection Date 2011-06-25
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Details Shutterless data collection, fine phi slicing experiments
    Collection Date 2012-08-09
     
    Diffraction Radiation
    Monochromator Double crystal Si(111)
    Diffraction Protocol SAD
    Monochromator Liquid nitrogen-cooled double crystal Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL9-2
    Wavelength List 0.97893
    Site SSRL
    Beamline BL9-2
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL12-2
    Wavelength List 0.95369
    Site SSRL
    Beamline BL12-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.06
    Observed Criterion Sigma(I) 0.34
    Resolution(High) 1.76
    Resolution(Low) 39.19
    Number Reflections(All) 951878
    Number Reflections(Observed) 837015
    Percent Possible(Observed) 88.0
    R Merge I(Observed) 0.123
    B(Isotropic) From Wilson Plot 29.29
    Redundancy 3.6
     
    High Resolution Shell Details
    Resolution(High) 1.76
    Resolution(Low) 1.86
    Percent Possible(All) 63.9
    Mean I Over Sigma(Observed) 0.4
    Redundancy 3.4
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 1.8
    Resolution(Low) 39.186
    Cut-off Sigma(F) 1.96
    Number of Reflections(Observed) 774229
    Number of Reflections(R-Free) 38896
    Percent Reflections(Observed) 86.87
    R-Factor(All) 0.195
    R-Factor(Observed) 0.1898
    R-Work 0.1883
    R-Free 0.2166
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 39.3211
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.8205
    Number of Reflections(R-Free) 388
    Number of Reflections(R-Work) 7442
    R-Factor(R-Work) 0.3498
    R-Factor(R-Free) 0.3717
    Percent Reflections(Observed) 26.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8205
    Shell Resolution(Low) 1.8419
    Number of Reflections(R-Free) 739
    Number of Reflections(R-Work) 13498
    R-Factor(R-Work) 0.3464
    R-Factor(R-Free) 0.3708
    Percent Reflections(Observed) 48.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8419
    Shell Resolution(Low) 1.8643
    Number of Reflections(R-Free) 1013
    Number of Reflections(R-Work) 20431
    R-Factor(R-Work) 0.3411
    R-Factor(R-Free) 0.3598
    Percent Reflections(Observed) 72.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8643
    Shell Resolution(Low) 1.8879
    Number of Reflections(R-Free) 1262
    Number of Reflections(R-Work) 24316
    R-Factor(R-Work) 0.3401
    R-Factor(R-Free) 0.366
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8879
    Shell Resolution(Low) 1.9128
    Number of Reflections(R-Free) 1369
    Number of Reflections(R-Work) 25031
    R-Factor(R-Work) 0.3269
    R-Factor(R-Free) 0.3492
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9128
    Shell Resolution(Low) 1.939
    Number of Reflections(R-Free) 1353
    Number of Reflections(R-Work) 25779
    R-Factor(R-Work) 0.3112
    R-Factor(R-Free) 0.3421
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.939
    Shell Resolution(Low) 1.9667
    Number of Reflections(R-Free) 1370
    Number of Reflections(R-Work) 25922
    R-Factor(R-Work) 0.2981
    R-Factor(R-Free) 0.32
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9667
    Shell Resolution(Low) 1.996
    Number of Reflections(R-Free) 1376
    Number of Reflections(R-Work) 25864
    R-Factor(R-Work) 0.2948
    R-Factor(R-Free) 0.3195
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.996
    Shell Resolution(Low) 2.0272
    Number of Reflections(R-Free) 1358
    Number of Reflections(R-Work) 25717
    R-Factor(R-Work) 0.2819
    R-Factor(R-Free) 0.3181
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0272
    Shell Resolution(Low) 2.0605
    Number of Reflections(R-Free) 1385
    Number of Reflections(R-Work) 25402
    R-Factor(R-Work) 0.2773
    R-Factor(R-Free) 0.3061
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0605
    Shell Resolution(Low) 2.096
    Number of Reflections(R-Free) 1321
    Number of Reflections(R-Work) 24714
    R-Factor(R-Work) 0.2669
    R-Factor(R-Free) 0.3031
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.096
    Shell Resolution(Low) 2.1341
    Number of Reflections(R-Free) 1261
    Number of Reflections(R-Work) 23661
    R-Factor(R-Work) 0.2452
    R-Factor(R-Free) 0.2886
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1341
    Shell Resolution(Low) 2.1751
    Number of Reflections(R-Free) 1393
    Number of Reflections(R-Work) 26685
    R-Factor(R-Work) 0.223
    R-Factor(R-Free) 0.2651
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1751
    Shell Resolution(Low) 2.2195
    Number of Reflections(R-Free) 1413
    Number of Reflections(R-Work) 26655
    R-Factor(R-Work) 0.2254
    R-Factor(R-Free) 0.2562
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2195
    Shell Resolution(Low) 2.2678
    Number of Reflections(R-Free) 1380
    Number of Reflections(R-Work) 26335
    R-Factor(R-Work) 0.2248
    R-Factor(R-Free) 0.2704
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2678
    Shell Resolution(Low) 2.3205
    Number of Reflections(R-Free) 1303
    Number of Reflections(R-Work) 26303
    R-Factor(R-Work) 0.2104
    R-Factor(R-Free) 0.2564
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3205
    Shell Resolution(Low) 2.3786
    Number of Reflections(R-Free) 1304
    Number of Reflections(R-Work) 26416
    R-Factor(R-Work) 0.2051
    R-Factor(R-Free) 0.2556
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3786
    Shell Resolution(Low) 2.4429
    Number of Reflections(R-Free) 1417
    Number of Reflections(R-Work) 25959
    R-Factor(R-Work) 0.2046
    R-Factor(R-Free) 0.252
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4429
    Shell Resolution(Low) 2.5147
    Number of Reflections(R-Free) 1321
    Number of Reflections(R-Work) 25295
    R-Factor(R-Work) 0.2035
    R-Factor(R-Free) 0.2492
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5147
    Shell Resolution(Low) 2.5959
    Number of Reflections(R-Free) 1252
    Number of Reflections(R-Work) 23382
    R-Factor(R-Work) 0.2071
    R-Factor(R-Free) 0.248
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5959
    Shell Resolution(Low) 2.6887
    Number of Reflections(R-Free) 1488
    Number of Reflections(R-Work) 26583
    R-Factor(R-Work) 0.199
    R-Factor(R-Free) 0.242
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6887
    Shell Resolution(Low) 2.7963
    Number of Reflections(R-Free) 1331
    Number of Reflections(R-Work) 26693
    R-Factor(R-Work) 0.1858
    R-Factor(R-Free) 0.2309
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7963
    Shell Resolution(Low) 2.9235
    Number of Reflections(R-Free) 1444
    Number of Reflections(R-Work) 26479
    R-Factor(R-Work) 0.1859
    R-Factor(R-Free) 0.222
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9235
    Shell Resolution(Low) 3.0776
    Number of Reflections(R-Free) 1402
    Number of Reflections(R-Work) 26199
    R-Factor(R-Work) 0.1854
    R-Factor(R-Free) 0.2183
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0776
    Shell Resolution(Low) 3.2703
    Number of Reflections(R-Free) 1308
    Number of Reflections(R-Work) 25354
    R-Factor(R-Work) 0.1812
    R-Factor(R-Free) 0.2165
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2703
    Shell Resolution(Low) 3.5227
    Number of Reflections(R-Free) 1273
    Number of Reflections(R-Work) 24780
    R-Factor(R-Work) 0.1711
    R-Factor(R-Free) 0.203
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5227
    Shell Resolution(Low) 3.8769
    Number of Reflections(R-Free) 1534
    Number of Reflections(R-Work) 26867
    R-Factor(R-Work) 0.1516
    R-Factor(R-Free) 0.177
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8769
    Shell Resolution(Low) 4.4372
    Number of Reflections(R-Free) 1400
    Number of Reflections(R-Work) 26320
    R-Factor(R-Work) 0.1285
    R-Factor(R-Free) 0.1475
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4372
    Shell Resolution(Low) 5.5878
    Number of Reflections(R-Free) 1330
    Number of Reflections(R-Work) 25098
    R-Factor(R-Work) 0.1266
    R-Factor(R-Free) 0.145
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5878
    Shell Resolution(Low) 39.1952
    Number of Reflections(R-Free) 1408
    Number of Reflections(R-Work) 26153
    R-Factor(R-Work) 0.1712
    R-Factor(R-Free) 0.1719
    Percent Reflections(Observed) 93.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 12.128
    f_plane_restr 0.004
    f_chiral_restr 0.084
    f_angle_d 1.18
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 58460
    Nucleic Acid Atoms 0
    Heterogen Atoms 300
    Solvent Atoms 4520
     
     
  •   Software and Computing Hide
    Computing
    Data Collection Blue Ice
    Data Reduction (intensity integration) XDS
    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