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X-RAY DIFFRACTION
Materials and Methods page
4EU3
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 8.2
    Temperature 298.0
    Details 0.9 M sodium citrate, 0.1 M imidazole, and 25 mM 2-mercaptoethanol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 67.48 α = 90
    b = 110.35 β = 90
    c = 119.84 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 MARMOSAIC 225 mm CCD
    Collection Date 2010-03-15
     
    Diffraction Radiation
    Monochromator C(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-F
    Wavelength List 0.97872
    Site APS
    Beamline 21-ID-F
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.58
    Resolution(Low) 50
    Number Reflections(All) 121024
    Number Reflections(Observed) 121024
    Percent Possible(Observed) 98.4
    R Merge I(Observed) 0.103
    Redundancy 12.4
     
    High Resolution Shell Details
    Resolution(High) 1.58
    Resolution(Low) 1.61
    Percent Possible(All) 86.0
    R Merge I(Observed) 0.442
    Mean I Over Sigma(Observed) 2.1
    R-Sym I(Observed) 0.442
    Redundancy 4.9
    Number Unique Reflections(All) 5211
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.58
    Resolution(Low) 40.234
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 120904
    Number of Reflections(R-Free) 6055
    Percent Reflections(Observed) 98.3
    R-Factor(Observed) 0.1573
    R-Work 0.1557
    R-Free 0.1887
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 14.3122
    Anisotropic B[1][1] -2.2324
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 4.0437
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -1.8113
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5796
    Shell Resolution(Low) 1.5976
    Number of Reflections(Observed) 3398
    Number of Reflections(R-Free) 196
    Number of Reflections(R-Work) 3202
    R-Factor(R-Work) 0.2578
    R-Factor(R-Free) 0.2983
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5976
    Shell Resolution(Low) 1.6163
    Number of Reflections(Observed) 3594
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 3421
    R-Factor(R-Work) 0.2661
    R-Factor(R-Free) 0.2904
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6163
    Shell Resolution(Low) 1.6361
    Number of Reflections(Observed) 3683
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3494
    R-Factor(R-Work) 0.2278
    R-Factor(R-Free) 0.2616
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6361
    Shell Resolution(Low) 1.6568
    Number of Reflections(Observed) 3797
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 3622
    R-Factor(R-Work) 0.2135
    R-Factor(R-Free) 0.2297
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6568
    Shell Resolution(Low) 1.6786
    Number of Reflections(Observed) 3895
    Number of Reflections(R-Free) 191
    Number of Reflections(R-Work) 3704
    R-Factor(R-Work) 0.2038
    R-Factor(R-Free) 0.2506
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6786
    Shell Resolution(Low) 1.7016
    Number of Reflections(Observed) 3937
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 3724
    R-Factor(R-Work) 0.1823
    R-Factor(R-Free) 0.2262
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7016
    Shell Resolution(Low) 1.7259
    Number of Reflections(Observed) 4020
    Number of Reflections(R-Free) 199
    Number of Reflections(R-Work) 3821
    R-Factor(R-Work) 0.1738
    R-Factor(R-Free) 0.2072
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7259
    Shell Resolution(Low) 1.7516
    Number of Reflections(Observed) 4042
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 3832
    R-Factor(R-Work) 0.167
    R-Factor(R-Free) 0.2082
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7516
    Shell Resolution(Low) 1.779
    Number of Reflections(Observed) 4097
    Number of Reflections(R-Free) 204
    Number of Reflections(R-Work) 3893
    R-Factor(R-Work) 0.1616
    R-Factor(R-Free) 0.1762
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.779
    Shell Resolution(Low) 1.8082
    Number of Reflections(Observed) 4046
    Number of Reflections(R-Free) 197
    Number of Reflections(R-Work) 3849
    R-Factor(R-Work) 0.1625
    R-Factor(R-Free) 0.2231
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8082
    Shell Resolution(Low) 1.8394
    Number of Reflections(Observed) 4067
    Number of Reflections(R-Free) 204
    Number of Reflections(R-Work) 3863
    R-Factor(R-Work) 0.1569
    R-Factor(R-Free) 0.2123
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8394
    Shell Resolution(Low) 1.8728
    Number of Reflections(Observed) 4097
    Number of Reflections(R-Free) 196
    Number of Reflections(R-Work) 3901
    R-Factor(R-Work) 0.1578
    R-Factor(R-Free) 0.2094
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8728
    Shell Resolution(Low) 1.9088
    Number of Reflections(Observed) 4017
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 3819
    R-Factor(R-Work) 0.1545
    R-Factor(R-Free) 0.2009
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9088
    Shell Resolution(Low) 1.9478
    Number of Reflections(Observed) 4053
    Number of Reflections(R-Free) 200
    Number of Reflections(R-Work) 3853
    R-Factor(R-Work) 0.1582
    R-Factor(R-Free) 0.2063
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9478
    Shell Resolution(Low) 1.9901
    Number of Reflections(Observed) 4112
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 3905
    R-Factor(R-Work) 0.154
    R-Factor(R-Free) 0.2077
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9901
    Shell Resolution(Low) 2.0364
    Number of Reflections(Observed) 4058
    Number of Reflections(R-Free) 206
    Number of Reflections(R-Work) 3852
    R-Factor(R-Work) 0.152
    R-Factor(R-Free) 0.1919
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0364
    Shell Resolution(Low) 2.0873
    Number of Reflections(Observed) 4071
    Number of Reflections(R-Free) 194
    Number of Reflections(R-Work) 3877
    R-Factor(R-Work) 0.1536
    R-Factor(R-Free) 0.1765
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0873
    Shell Resolution(Low) 2.1438
    Number of Reflections(Observed) 4101
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 3891
    R-Factor(R-Work) 0.1485
    R-Factor(R-Free) 0.1847
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1438
    Shell Resolution(Low) 2.2069
    Number of Reflections(Observed) 4107
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 3897
    R-Factor(R-Work) 0.1522
    R-Factor(R-Free) 0.1774
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2069
    Shell Resolution(Low) 2.2781
    Number of Reflections(Observed) 4059
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 3851
    R-Factor(R-Work) 0.1533
    R-Factor(R-Free) 0.1895
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2781
    Shell Resolution(Low) 2.3595
    Number of Reflections(Observed) 4116
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 3901
    R-Factor(R-Work) 0.1559
    R-Factor(R-Free) 0.1826
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3595
    Shell Resolution(Low) 2.454
    Number of Reflections(Observed) 4109
    Number of Reflections(R-Free) 188
    Number of Reflections(R-Work) 3921
    R-Factor(R-Work) 0.1472
    R-Factor(R-Free) 0.184
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.454
    Shell Resolution(Low) 2.5656
    Number of Reflections(Observed) 4090
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 3883
    R-Factor(R-Work) 0.1528
    R-Factor(R-Free) 0.2071
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5656
    Shell Resolution(Low) 2.7009
    Number of Reflections(Observed) 4127
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 3916
    R-Factor(R-Work) 0.1576
    R-Factor(R-Free) 0.183
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7009
    Shell Resolution(Low) 2.87
    Number of Reflections(Observed) 4114
    Number of Reflections(R-Free) 197
    Number of Reflections(R-Work) 3917
    R-Factor(R-Work) 0.1622
    R-Factor(R-Free) 0.1851
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.87
    Shell Resolution(Low) 3.0916
    Number of Reflections(Observed) 4153
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 3950
    R-Factor(R-Work) 0.1566
    R-Factor(R-Free) 0.1958
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0916
    Shell Resolution(Low) 3.4025
    Number of Reflections(Observed) 4159
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 3947
    R-Factor(R-Work) 0.1467
    R-Factor(R-Free) 0.1549
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4025
    Shell Resolution(Low) 3.8945
    Number of Reflections(Observed) 4171
    Number of Reflections(R-Free) 214
    Number of Reflections(R-Work) 3957
    R-Factor(R-Work) 0.1264
    R-Factor(R-Free) 0.1564
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8945
    Shell Resolution(Low) 4.9053
    Number of Reflections(Observed) 4231
    Number of Reflections(R-Free) 204
    Number of Reflections(R-Work) 4027
    R-Factor(R-Work) 0.1231
    R-Factor(R-Free) 0.1498
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9053
    Shell Resolution(Low) 40.2468
    Number of Reflections(Observed) 4383
    Number of Reflections(R-Free) 224
    Number of Reflections(R-Work) 4159
    R-Factor(R-Work) 0.1567
    R-Factor(R-Free) 0.1805
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 12.507
    f_plane_restr 0.005
    f_chiral_restr 0.074
    f_angle_d 1.068
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 7768
    Nucleic Acid Atoms 0
    Heterogen Atoms 17
    Solvent Atoms 1272
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHENIX
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL