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X-RAY DIFFRACTION
Materials and Methods page
3GZO
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 298.0
    Details 2.4 M sodium malonate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 166.15 α = 90
    b = 203.26 β = 90
    c = 143.32 γ = 90
     
    Space Group
    Space Group Name:    C 2 2 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type RIGAKU RAXIS VII
    Details mirrors
    Collection Date 2003-10-09
     
    Diffraction Radiation
    Monochromator confocal optics
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU FR-D
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.1
    Resolution(Low) 50
    Number Reflections(Observed) 140272
    Percent Possible(Observed) 99.8
    B(Isotropic) From Wilson Plot 20.6
    Redundancy 3.5
     
    High Resolution Shell Details
    Resolution(High) 2.1
    Resolution(Low) 2.18
    Percent Possible(All) 99.6
    Mean I Over Sigma(Observed) 2.3
    R-Sym I(Observed) 0.508
    Redundancy 3.2
    Number Unique Reflections(All) 13842
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.1
    Resolution(Low) 41.492
    Cut-off Sigma(F) 0.02
    Number of Reflections(Observed) 135446
    Number of Reflections(R-Free) 6759
    Percent Reflections(Observed) 96.34
    R-Factor(Observed) 0.1737
    R-Work 0.1716
    R-Free 0.2136
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model ISOTROPIC
    Mean Isotropic B Value 25.7
    Anisotropic B[1][1] -1.4361
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -2.0683
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 3.2778
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1
    Shell Resolution(Low) 2.1243
    Number of Reflections(R-Free) 201
    Number of Reflections(R-Work) 4007
    R-Factor(R-Work) 0.2522
    R-Factor(R-Free) 0.2955
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1243
    Shell Resolution(Low) 2.1493
    Number of Reflections(R-Free) 210
    Number of Reflections(R-Work) 4129
    R-Factor(R-Work) 0.2443
    R-Factor(R-Free) 0.2989
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1493
    Shell Resolution(Low) 2.1756
    Number of Reflections(R-Free) 214
    Number of Reflections(R-Work) 4091
    R-Factor(R-Work) 0.2418
    R-Factor(R-Free) 0.267
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1756
    Shell Resolution(Low) 2.2031
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 4143
    R-Factor(R-Work) 0.2362
    R-Factor(R-Free) 0.2723
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2031
    Shell Resolution(Low) 2.2321
    Number of Reflections(R-Free) 232
    Number of Reflections(R-Work) 4159
    R-Factor(R-Work) 0.2402
    R-Factor(R-Free) 0.2759
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2321
    Shell Resolution(Low) 2.2627
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 4163
    R-Factor(R-Work) 0.2283
    R-Factor(R-Free) 0.2788
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2627
    Shell Resolution(Low) 2.295
    Number of Reflections(R-Free) 187
    Number of Reflections(R-Work) 4156
    R-Factor(R-Work) 0.2208
    R-Factor(R-Free) 0.2761
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.295
    Shell Resolution(Low) 2.3292
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 4183
    R-Factor(R-Work) 0.2116
    R-Factor(R-Free) 0.2476
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3292
    Shell Resolution(Low) 2.3656
    Number of Reflections(R-Free) 213
    Number of Reflections(R-Work) 4220
    R-Factor(R-Work) 0.2202
    R-Factor(R-Free) 0.2828
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3656
    Shell Resolution(Low) 2.4044
    Number of Reflections(R-Free) 221
    Number of Reflections(R-Work) 4189
    R-Factor(R-Work) 0.2144
    R-Factor(R-Free) 0.275
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4044
    Shell Resolution(Low) 2.4459
    Number of Reflections(R-Free) 248
    Number of Reflections(R-Work) 4203
    R-Factor(R-Work) 0.2139
    R-Factor(R-Free) 0.2534
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4459
    Shell Resolution(Low) 2.4903
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 4242
    R-Factor(R-Work) 0.209
    R-Factor(R-Free) 0.2766
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4903
    Shell Resolution(Low) 2.5382
    Number of Reflections(R-Free) 214
    Number of Reflections(R-Work) 4276
    R-Factor(R-Work) 0.2076
    R-Factor(R-Free) 0.2625
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5382
    Shell Resolution(Low) 2.59
    Number of Reflections(R-Free) 257
    Number of Reflections(R-Work) 4208
    R-Factor(R-Work) 0.203
    R-Factor(R-Free) 0.2475
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.59
    Shell Resolution(Low) 2.6463
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 4238
    R-Factor(R-Work) 0.2002
    R-Factor(R-Free) 0.2567
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6463
    Shell Resolution(Low) 2.7079
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4238
    R-Factor(R-Work) 0.1965
    R-Factor(R-Free) 0.2568
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7079
    Shell Resolution(Low) 2.7756
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4338
    R-Factor(R-Work) 0.1816
    R-Factor(R-Free) 0.2439
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7756
    Shell Resolution(Low) 2.8506
    Number of Reflections(R-Free) 219
    Number of Reflections(R-Work) 4323
    R-Factor(R-Work) 0.1773
    R-Factor(R-Free) 0.2168
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8506
    Shell Resolution(Low) 2.9345
    Number of Reflections(R-Free) 223
    Number of Reflections(R-Work) 4350
    R-Factor(R-Work) 0.1812
    R-Factor(R-Free) 0.2071
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9345
    Shell Resolution(Low) 3.0292
    Number of Reflections(R-Free) 243
    Number of Reflections(R-Work) 4332
    R-Factor(R-Work) 0.1711
    R-Factor(R-Free) 0.2141
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0292
    Shell Resolution(Low) 3.1374
    Number of Reflections(R-Free) 241
    Number of Reflections(R-Work) 4368
    R-Factor(R-Work) 0.1604
    R-Factor(R-Free) 0.2195
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1374
    Shell Resolution(Low) 3.263
    Number of Reflections(R-Free) 220
    Number of Reflections(R-Work) 4374
    R-Factor(R-Work) 0.1507
    R-Factor(R-Free) 0.1915
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.263
    Shell Resolution(Low) 3.4114
    Number of Reflections(R-Free) 237
    Number of Reflections(R-Work) 4414
    R-Factor(R-Work) 0.1401
    R-Factor(R-Free) 0.1809
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4114
    Shell Resolution(Low) 3.5912
    Number of Reflections(R-Free) 242
    Number of Reflections(R-Work) 4398
    R-Factor(R-Work) 0.1382
    R-Factor(R-Free) 0.1823
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5912
    Shell Resolution(Low) 3.816
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 4455
    R-Factor(R-Work) 0.13
    R-Factor(R-Free) 0.1611
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.816
    Shell Resolution(Low) 4.1104
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4430
    R-Factor(R-Work) 0.1222
    R-Factor(R-Free) 0.1629
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1104
    Shell Resolution(Low) 4.5236
    Number of Reflections(R-Free) 231
    Number of Reflections(R-Work) 4469
    R-Factor(R-Work) 0.1147
    R-Factor(R-Free) 0.1438
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5236
    Shell Resolution(Low) 5.1771
    Number of Reflections(R-Free) 228
    Number of Reflections(R-Work) 4458
    R-Factor(R-Work) 0.12
    R-Factor(R-Free) 0.1398
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.1771
    Shell Resolution(Low) 6.5185
    Number of Reflections(R-Free) 217
    Number of Reflections(R-Work) 4508
    R-Factor(R-Work) 0.1446
    R-Factor(R-Free) 0.175
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.5185
    Shell Resolution(Low) 41.5006
    Number of Reflections(R-Free) 226
    Number of Reflections(R-Work) 4625
    R-Factor(R-Work) 0.1668
    R-Factor(R-Free) 0.1977
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_angle_deg 1.159
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 11140
    Nucleic Acid Atoms 0
    Heterogen Atoms 39
    Solvent Atoms 1621
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CrystalClear
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution MOLREP
    Structure Refinement PHENIX (phenix.refine: 1.4_4)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.4_4)
    model building MOLREP
    data collection CrystalClear