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X-RAY DIFFRACTION
Materials and Methods page
4HL1
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Temperature 289.0
    Details B11: 0.2 M lithium sulfate, 0.1 M Bis-TrisHCl pH 6.5, 25 %(w/v) PEG 3350, 5 mM CdCl2, 100mM ampicillin, VAPOR DIFFUSION, SITTING DROP, temperature 289K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 39 α = 90
    b = 78.7 β = 90
    c = 134.38 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 ADSC QUANTUM 315r
    Details mirrors
    Collection Date 2011-10-09
     
    Diffraction Radiation
    Monochromator double crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength List 0.97924
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.5
    Resolution(Low) 50
    Number Reflections(Observed) 123712
    Percent Possible(Observed) 98.2
    B(Isotropic) From Wilson Plot 13.0
    Redundancy 6.2
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.53
    Percent Possible(All) 93.5
    Mean I Over Sigma(Observed) 2.1
    R-Sym I(Observed) 0.782
    Redundancy 4.1
    Number Unique Reflections(All) 3509
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.5
    Resolution(Low) 34.942
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 123712
    Number of Reflections(Observed) 123712
    Number of Reflections(R-Free) 6300
    Percent Reflections(Observed) 96.72
    R-Factor(All) 0.137
    R-Factor(Observed) 0.137
    R-Work 0.137
    R-Free 0.149
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Isotropic Thermal Model mixed
    Mean Isotropic B Value 18.9
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5
    Shell Resolution(Low) 1.5171
    Number of Reflections(Observed) 3569
    Number of Reflections(R-Free) 225
    Number of Reflections(R-Work) 3344
    R-Factor(R-Work) 0.2355
    R-Factor(R-Free) 0.255
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5171
    Shell Resolution(Low) 1.5349
    Number of Reflections(Observed) 3814
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 3606
    R-Factor(R-Work) 0.221
    R-Factor(R-Free) 0.2277
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5349
    Shell Resolution(Low) 1.5537
    Number of Reflections(Observed) 3920
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 3725
    R-Factor(R-Work) 0.1975
    R-Factor(R-Free) 0.2067
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5537
    Shell Resolution(Low) 1.5733
    Number of Reflections(Observed) 3961
    Number of Reflections(R-Free) 184
    Number of Reflections(R-Work) 3777
    R-Factor(R-Work) 0.1844
    R-Factor(R-Free) 0.1901
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5733
    Shell Resolution(Low) 1.594
    Number of Reflections(Observed) 4021
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 3867
    R-Factor(R-Work) 0.173
    R-Factor(R-Free) 0.199
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.594
    Shell Resolution(Low) 1.6159
    Number of Reflections(Observed) 4057
    Number of Reflections(R-Free) 200
    Number of Reflections(R-Work) 3857
    R-Factor(R-Work) 0.165
    R-Factor(R-Free) 0.1892
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6159
    Shell Resolution(Low) 1.6389
    Number of Reflections(Observed) 4036
    Number of Reflections(R-Free) 215
    Number of Reflections(R-Work) 3821
    R-Factor(R-Work) 0.1541
    R-Factor(R-Free) 0.1457
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6389
    Shell Resolution(Low) 1.6634
    Number of Reflections(Observed) 4129
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 3892
    R-Factor(R-Work) 0.1499
    R-Factor(R-Free) 0.1702
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6634
    Shell Resolution(Low) 1.6894
    Number of Reflections(Observed) 4101
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 3906
    R-Factor(R-Work) 0.1483
    R-Factor(R-Free) 0.1942
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6894
    Shell Resolution(Low) 1.7171
    Number of Reflections(Observed) 4010
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 3829
    R-Factor(R-Work) 0.1466
    R-Factor(R-Free) 0.1449
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7171
    Shell Resolution(Low) 1.7467
    Number of Reflections(Observed) 4142
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 3947
    R-Factor(R-Work) 0.143
    R-Factor(R-Free) 0.1942
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7467
    Shell Resolution(Low) 1.7785
    Number of Reflections(Observed) 4130
    Number of Reflections(R-Free) 233
    Number of Reflections(R-Work) 3897
    R-Factor(R-Work) 0.1328
    R-Factor(R-Free) 0.1666
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7785
    Shell Resolution(Low) 1.8127
    Number of Reflections(Observed) 4136
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3950
    R-Factor(R-Work) 0.129
    R-Factor(R-Free) 0.1606
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8127
    Shell Resolution(Low) 1.8497
    Number of Reflections(Observed) 4187
    Number of Reflections(R-Free) 234
    Number of Reflections(R-Work) 3953
    R-Factor(R-Work) 0.1274
    R-Factor(R-Free) 0.1421
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8497
    Shell Resolution(Low) 1.8899
    Number of Reflections(Observed) 4149
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 3941
    R-Factor(R-Work) 0.1339
    R-Factor(R-Free) 0.1352
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8899
    Shell Resolution(Low) 1.9338
    Number of Reflections(Observed) 4164
    Number of Reflections(R-Free) 207
    Number of Reflections(R-Work) 3957
    R-Factor(R-Work) 0.135
    R-Factor(R-Free) 0.1483
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9338
    Shell Resolution(Low) 1.9822
    Number of Reflections(Observed) 4206
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 3977
    R-Factor(R-Work) 0.1294
    R-Factor(R-Free) 0.1443
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9822
    Shell Resolution(Low) 2.0358
    Number of Reflections(Observed) 4206
    Number of Reflections(R-Free) 202
    Number of Reflections(R-Work) 4004
    R-Factor(R-Work) 0.1229
    R-Factor(R-Free) 0.1404
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0358
    Shell Resolution(Low) 2.0957
    Number of Reflections(Observed) 4190
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 3992
    R-Factor(R-Work) 0.1294
    R-Factor(R-Free) 0.1449
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0957
    Shell Resolution(Low) 2.1633
    Number of Reflections(Observed) 4262
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 4036
    R-Factor(R-Work) 0.122
    R-Factor(R-Free) 0.1429
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1633
    Shell Resolution(Low) 2.2406
    Number of Reflections(Observed) 4194
    Number of Reflections(R-Free) 282
    Number of Reflections(R-Work) 3912
    R-Factor(R-Work) 0.1217
    R-Factor(R-Free) 0.1118
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2406
    Shell Resolution(Low) 2.3303
    Number of Reflections(Observed) 4223
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 3995
    R-Factor(R-Work) 0.1257
    R-Factor(R-Free) 0.1293
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3303
    Shell Resolution(Low) 2.4363
    Number of Reflections(Observed) 4272
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 4062
    R-Factor(R-Work) 0.1306
    R-Factor(R-Free) 0.1311
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4363
    Shell Resolution(Low) 2.5648
    Number of Reflections(Observed) 4228
    Number of Reflections(R-Free) 218
    Number of Reflections(R-Work) 4010
    R-Factor(R-Work) 0.134
    R-Factor(R-Free) 0.1626
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5648
    Shell Resolution(Low) 2.7254
    Number of Reflections(Observed) 4235
    Number of Reflections(R-Free) 205
    Number of Reflections(R-Work) 4030
    R-Factor(R-Work) 0.1368
    R-Factor(R-Free) 0.1405
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7254
    Shell Resolution(Low) 2.9357
    Number of Reflections(Observed) 4244
    Number of Reflections(R-Free) 208
    Number of Reflections(R-Work) 4036
    R-Factor(R-Work) 0.1389
    R-Factor(R-Free) 0.1723
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9357
    Shell Resolution(Low) 3.231
    Number of Reflections(Observed) 4264
    Number of Reflections(R-Free) 211
    Number of Reflections(R-Work) 4053
    R-Factor(R-Work) 0.1365
    R-Factor(R-Free) 0.1366
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.231
    Shell Resolution(Low) 3.698
    Number of Reflections(Observed) 4221
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 3989
    R-Factor(R-Work) 0.1249
    R-Factor(R-Free) 0.1573
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.698
    Shell Resolution(Low) 4.6574
    Number of Reflections(Observed) 4238
    Number of Reflections(R-Free) 196
    Number of Reflections(R-Work) 4042
    R-Factor(R-Work) 0.1197
    R-Factor(R-Free) 0.1284
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6574
    Shell Resolution(Low) 34.9519
    Number of Reflections(Observed) 4203
    Number of Reflections(R-Free) 198
    Number of Reflections(R-Work) 4005
    R-Factor(R-Work) 0.1475
    R-Factor(R-Free) 0.143
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.097
    f_dihedral_angle_d 14.268
    f_angle_d 1.581
    f_bond_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3557
    Nucleic Acid Atoms 0
    Heterogen Atoms 52
    Solvent Atoms 469
     
     
  •   Software and Computing Hide
    Computing
    Data Collection SBCCOLLECT, HKL3000
    Data Reduction (intensity integration) HKL-3000
    Data Reduction (data scaling) HKL-3000
    Structure Solution HKL3000, Molrep
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1161)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.1_1161)
    model building Molrep
    model building HKL3000
    data collection HKL3000
    data collection SBCCOLLECT