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X-RAY DIFFRACTION
Materials and Methods page
4IT5
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6.5
    Temperature 291.0
    Details 0.1 M calcium acetate, 0.1 M cacodylate buffer, 40% PEG-3000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 55.43 α = 90
    b = 100.71 β = 90.47
    c = 70.35 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2009-03-29
     
    Diffraction Radiation
    Monochromator double crystal monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 19-ID
    Wavelength List 0.9792
    Site APS
    Beamline 19-ID
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.15
    Resolution(Low) 48.6
    Number Reflections(All) 41638
    Number Reflections(Observed) 41638
    Percent Possible(Observed) 99.3
    R Merge I(Observed) 0.094
    B(Isotropic) From Wilson Plot 50.4
    Redundancy 12.0
     
    High Resolution Shell Details
    Resolution(High) 2.15
    Resolution(Low) 2.19
    Percent Possible(All) 92.8
    R Merge I(Observed) 0.772
    Mean I Over Sigma(Observed) 2.41
    Redundancy 8.5
    Number Unique Reflections(All) 1935
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.152
    Resolution(Low) 48.56
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 1.89
    Number of Reflections(all) 81461
    Number of Reflections(Observed) 41550
    Number of Reflections(R-Free) 4126
    Percent Reflections(Observed) 98.64
    R-Factor(Observed) 0.2218
    R-Work 0.2198
    R-Free 0.2585
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 61.1333
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1518
    Shell Resolution(Low) 2.1771
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2275
    R-Factor(R-Work) 0.3123
    R-Factor(R-Free) 0.3892
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1771
    Shell Resolution(Low) 2.2036
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2552
    R-Factor(R-Work) 0.2935
    R-Factor(R-Free) 0.3451
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2036
    Shell Resolution(Low) 2.2315
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2526
    R-Factor(R-Work) 0.2906
    R-Factor(R-Free) 0.3215
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2315
    Shell Resolution(Low) 2.2609
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2552
    R-Factor(R-Work) 0.2841
    R-Factor(R-Free) 0.2931
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2609
    Shell Resolution(Low) 2.2919
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 2718
    R-Factor(R-Work) 0.2695
    R-Factor(R-Free) 0.3952
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2919
    Shell Resolution(Low) 2.3246
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 2628
    R-Factor(R-Work) 0.2721
    R-Factor(R-Free) 0.292
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3246
    Shell Resolution(Low) 2.3593
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 2720
    R-Factor(R-Work) 0.259
    R-Factor(R-Free) 0.2777
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3593
    Shell Resolution(Low) 2.3962
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 2718
    R-Factor(R-Work) 0.254
    R-Factor(R-Free) 0.3297
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3962
    Shell Resolution(Low) 2.4354
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 2632
    R-Factor(R-Work) 0.2546
    R-Factor(R-Free) 0.3244
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4354
    Shell Resolution(Low) 2.4774
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2678
    R-Factor(R-Work) 0.2357
    R-Factor(R-Free) 0.3103
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4774
    Shell Resolution(Low) 2.5225
    Number of Reflections(R-Free) 103
    Number of Reflections(R-Work) 2786
    R-Factor(R-Work) 0.2281
    R-Factor(R-Free) 0.2598
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5225
    Shell Resolution(Low) 2.571
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2626
    R-Factor(R-Work) 0.2436
    R-Factor(R-Free) 0.2708
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.571
    Shell Resolution(Low) 2.6235
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2747
    R-Factor(R-Work) 0.24
    R-Factor(R-Free) 0.313
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6235
    Shell Resolution(Low) 2.6805
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2655
    R-Factor(R-Work) 0.2334
    R-Factor(R-Free) 0.311
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6805
    Shell Resolution(Low) 2.7429
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2746
    R-Factor(R-Work) 0.2462
    R-Factor(R-Free) 0.2755
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7429
    Shell Resolution(Low) 2.8114
    Number of Reflections(R-Free) 114
    Number of Reflections(R-Work) 2721
    R-Factor(R-Work) 0.2467
    R-Factor(R-Free) 0.2935
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8114
    Shell Resolution(Low) 2.8875
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2695
    R-Factor(R-Work) 0.2468
    R-Factor(R-Free) 0.3007
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8875
    Shell Resolution(Low) 2.9724
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2693
    R-Factor(R-Work) 0.245
    R-Factor(R-Free) 0.294
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9724
    Shell Resolution(Low) 3.0683
    Number of Reflections(R-Free) 111
    Number of Reflections(R-Work) 2754
    R-Factor(R-Work) 0.2619
    R-Factor(R-Free) 0.3541
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0683
    Shell Resolution(Low) 3.178
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 2619
    R-Factor(R-Work) 0.2524
    R-Factor(R-Free) 0.3106
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.178
    Shell Resolution(Low) 3.3052
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2729
    R-Factor(R-Work) 0.2483
    R-Factor(R-Free) 0.3091
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3052
    Shell Resolution(Low) 3.4556
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2695
    R-Factor(R-Work) 0.2306
    R-Factor(R-Free) 0.286
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4556
    Shell Resolution(Low) 3.6377
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2703
    R-Factor(R-Work) 0.2178
    R-Factor(R-Free) 0.2175
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6377
    Shell Resolution(Low) 3.8655
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 2706
    R-Factor(R-Work) 0.2012
    R-Factor(R-Free) 0.2361
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8655
    Shell Resolution(Low) 4.1638
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2671
    R-Factor(R-Work) 0.1892
    R-Factor(R-Free) 0.2431
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1638
    Shell Resolution(Low) 4.5826
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2734
    R-Factor(R-Work) 0.1748
    R-Factor(R-Free) 0.1879
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5826
    Shell Resolution(Low) 5.245
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2677
    R-Factor(R-Work) 0.1903
    R-Factor(R-Free) 0.213
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.245
    Shell Resolution(Low) 6.6055
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2700
    R-Factor(R-Work) 0.2308
    R-Factor(R-Free) 0.2953
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.6055
    Shell Resolution(Low) 48.5721
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2679
    R-Factor(R-Work) 0.1816
    R-Factor(R-Free) 0.2008
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 18.973
    f_plane_restr 0.002
    f_chiral_restr 0.047
    f_angle_d 0.702
    f_bond_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5373
    Nucleic Acid Atoms 0
    Heterogen Atoms 5
    Solvent Atoms 91
     
     
  •   Software and Computing Hide
    Computing
    Data Collection SBC-collect
    Data Reduction (intensity integration) HKL-3000
    Data Reduction (data scaling) HKL-3000
    Structure Solution SHELXD, MLPHARE, DM, SOLVE/RESOLVE, HKL-3000
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction HKL