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X-RAY DIFFRACTION
Materials and Methods page
4DR4
  •   Crystallization Hide
    Crystallization Experiments
    Method HANGING DROP
    pH 6.5
    Temperature 277.0
    Details MPD, pH 6.5, HANGING DROP, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 400.95 α = 90
    b = 400.95 β = 90
    c = 176.68 γ = 90
     
    Space Group
    Space Group Name:    P 41 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2008-12-03
     
    Diffraction Radiation
    Monochromator Kohzu HLD8-24
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-C
    Wavelength List 0.98
    Site APS
    Beamline 24-ID-C
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) -3.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.97
    Resolution(Low) 50
    Number Reflections(All) 123861
    Number Reflections(Observed) 123861
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.253
    Redundancy 7.3
     
    High Resolution Shell Details
    Resolution(High) 3.969
    Resolution(Low) 4.04
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.992
    Redundancy 6.7
    Number Unique Reflections(All) 6102
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method FOURIER SYNTHESIS
    reflnsShellList 3.969
    Resolution(Low) 49.732
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 123736
    Number of Reflections(Observed) 123736
    Number of Reflections(R-Free) 6187
    Percent Reflections(Observed) 99.94
    R-Factor(Observed) 0.1561
    R-Work 0.1531
    R-Free 0.2124
    R-Free Selection Details FROM PDB ENTRY 2VQE
     
    Temperature Factor Modeling
    Mean Isotropic B Value 101.162
    Anisotropic B[1][1] -12.2147
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -12.2147
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 2.7328
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.969
    Shell Resolution(Low) 4.0144
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 3867
    R-Factor(R-Work) 0.2245
    R-Factor(R-Free) 0.3026
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0144
    Shell Resolution(Low) 4.0616
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 3825
    R-Factor(R-Work) 0.2142
    R-Factor(R-Free) 0.3067
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0616
    Shell Resolution(Low) 4.1111
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 3862
    R-Factor(R-Work) 0.2053
    R-Factor(R-Free) 0.2691
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1111
    Shell Resolution(Low) 4.1632
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 3866
    R-Factor(R-Work) 0.182
    R-Factor(R-Free) 0.2414
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1632
    Shell Resolution(Low) 4.2179
    Number of Reflections(R-Free) 201
    Number of Reflections(R-Work) 3913
    R-Factor(R-Work) 0.1735
    R-Factor(R-Free) 0.2509
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2179
    Shell Resolution(Low) 4.2757
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 3865
    R-Factor(R-Work) 0.1678
    R-Factor(R-Free) 0.248
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2757
    Shell Resolution(Low) 4.3367
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 3887
    R-Factor(R-Work) 0.1729
    R-Factor(R-Free) 0.2522
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3367
    Shell Resolution(Low) 4.4014
    Number of Reflections(R-Free) 227
    Number of Reflections(R-Work) 3852
    R-Factor(R-Work) 0.1744
    R-Factor(R-Free) 0.2364
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4014
    Shell Resolution(Low) 4.4701
    Number of Reflections(R-Free) 212
    Number of Reflections(R-Work) 3855
    R-Factor(R-Work) 0.151
    R-Factor(R-Free) 0.235
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4701
    Shell Resolution(Low) 4.5434
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 3895
    R-Factor(R-Work) 0.1575
    R-Factor(R-Free) 0.2215
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5434
    Shell Resolution(Low) 4.6217
    Number of Reflections(R-Free) 191
    Number of Reflections(R-Work) 3888
    R-Factor(R-Work) 0.1482
    R-Factor(R-Free) 0.223
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6217
    Shell Resolution(Low) 4.7056
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 3892
    R-Factor(R-Work) 0.142
    R-Factor(R-Free) 0.1844
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7056
    Shell Resolution(Low) 4.7961
    Number of Reflections(R-Free) 193
    Number of Reflections(R-Work) 3910
    R-Factor(R-Work) 0.1401
    R-Factor(R-Free) 0.2231
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7961
    Shell Resolution(Low) 4.8939
    Number of Reflections(R-Free) 192
    Number of Reflections(R-Work) 3915
    R-Factor(R-Work) 0.1388
    R-Factor(R-Free) 0.2201
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.8939
    Shell Resolution(Low) 5.0002
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 3868
    R-Factor(R-Work) 0.1265
    R-Factor(R-Free) 0.1951
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0002
    Shell Resolution(Low) 5.1164
    Number of Reflections(R-Free) 192
    Number of Reflections(R-Work) 3908
    R-Factor(R-Work) 0.1276
    R-Factor(R-Free) 0.1865
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1164
    Shell Resolution(Low) 5.2442
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 3914
    R-Factor(R-Work) 0.1239
    R-Factor(R-Free) 0.1894
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2442
    Shell Resolution(Low) 5.3859
    Number of Reflections(R-Free) 199
    Number of Reflections(R-Work) 3911
    R-Factor(R-Work) 0.1161
    R-Factor(R-Free) 0.1724
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.3859
    Shell Resolution(Low) 5.5441
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 3924
    R-Factor(R-Work) 0.1094
    R-Factor(R-Free) 0.1859
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.5441
    Shell Resolution(Low) 5.7228
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 3891
    R-Factor(R-Work) 0.1114
    R-Factor(R-Free) 0.1746
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.7228
    Shell Resolution(Low) 5.9271
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 3936
    R-Factor(R-Work) 0.1155
    R-Factor(R-Free) 0.1903
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.9271
    Shell Resolution(Low) 6.164
    Number of Reflections(R-Free) 197
    Number of Reflections(R-Work) 3930
    R-Factor(R-Work) 0.1166
    R-Factor(R-Free) 0.1907
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.164
    Shell Resolution(Low) 6.4439
    Number of Reflections(R-Free) 192
    Number of Reflections(R-Work) 3947
    R-Factor(R-Work) 0.1169
    R-Factor(R-Free) 0.1673
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.4439
    Shell Resolution(Low) 6.7829
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 3926
    R-Factor(R-Work) 0.1186
    R-Factor(R-Free) 0.1969
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.7829
    Shell Resolution(Low) 7.2067
    Number of Reflections(R-Free) 201
    Number of Reflections(R-Work) 3938
    R-Factor(R-Work) 0.1109
    R-Factor(R-Free) 0.1777
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.2067
    Shell Resolution(Low) 7.7612
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 3986
    R-Factor(R-Work) 0.1178
    R-Factor(R-Free) 0.1643
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.7612
    Shell Resolution(Low) 8.5387
    Number of Reflections(R-Free) 209
    Number of Reflections(R-Work) 3976
    R-Factor(R-Work) 0.1301
    R-Factor(R-Free) 0.1848
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 8.5387
    Shell Resolution(Low) 9.7661
    Number of Reflections(R-Free) 230
    Number of Reflections(R-Work) 3988
    R-Factor(R-Work) 0.1461
    R-Factor(R-Free) 0.205
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 9.7661
    Shell Resolution(Low) 12.2736
    Number of Reflections(R-Free) 204
    Number of Reflections(R-Work) 4023
    R-Factor(R-Work) 0.1621
    R-Factor(R-Free) 0.1983
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 12.2736
    Shell Resolution(Low) 49.7357
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 4191
    R-Factor(R-Work) 0.2594
    R-Factor(R-Free) 0.2554
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 26.098
    f_plane_restr 0.008
    f_chiral_restr 0.083
    f_angle_d 1.527
    f_bond_d 0.013
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19152
    Nucleic Acid Atoms 32880
    Heterogen Atoms 1115
    Solvent Atoms 498
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHENIX (phenix.refine: dev_978)
    Structure Refinement PHENIX (phenix.refine: dev_978)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    data reduction SCALEPACK
    data collection DENZO