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X-RAY DIFFRACTION
Materials and Methods page
4H6P
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 295.0
    Details 1:1 mixture of protein (~12 mg/mL) in 100 mM NaCl, 20 mM TrisHCl, 1 mM DTT, pH 7 and precipatant (Emerald BioSystems) 25% w/v PEG3350, 4% isopropanol, 0.1 M HEPES (pH 7.5) 0.1 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 94.92 α = 90
    b = 287.59 β = 90
    c = 91.36 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2012-04-19
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type NSLS BEAMLINE X29A
    Wavelength List 0.9792
    Site NSLS
    Beamline X29A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.56
    Resolution(Low) 49.19
    Number Reflections(All) 85635
    Number Reflections(Observed) 85635
    Percent Possible(Observed) 100.0
     
    High Resolution Shell Details
    Resolution(High) 2.556
    Resolution(Low) 2.5865
    Percent Possible(All) 89.0
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.556
    Resolution(Low) 49.191
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 85635
    Number of Reflections(Observed) 81546
    Number of Reflections(R-Free) 4089
    Percent Reflections(Observed) 99.6
    R-Factor(Observed) 0.2348
    R-Work 0.2328
    R-Free 0.2712
    R-Free Selection Details random
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5564
    Shell Resolution(Low) 2.5865
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2362
    R-Factor(R-Work) 0.2966
    R-Factor(R-Free) 0.3296
    Percent Reflections(Observed) 89.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5865
    Shell Resolution(Low) 2.618
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2621
    R-Factor(R-Work) 0.2795
    R-Factor(R-Free) 0.3419
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.618
    Shell Resolution(Low) 2.6511
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2622
    R-Factor(R-Work) 0.2733
    R-Factor(R-Free) 0.3318
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6511
    Shell Resolution(Low) 2.686
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.2658
    R-Factor(R-Free) 0.2914
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.686
    Shell Resolution(Low) 2.7228
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2609
    R-Factor(R-Work) 0.2663
    R-Factor(R-Free) 0.3071
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7228
    Shell Resolution(Low) 2.7617
    Number of Reflections(R-Free) 126
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.2639
    R-Factor(R-Free) 0.2982
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7617
    Shell Resolution(Low) 2.8029
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.2568
    R-Factor(R-Free) 0.3314
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8029
    Shell Resolution(Low) 2.8467
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2657
    R-Factor(R-Work) 0.2577
    R-Factor(R-Free) 0.2761
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8467
    Shell Resolution(Low) 2.8934
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.269
    R-Factor(R-Free) 0.3045
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8934
    Shell Resolution(Low) 2.9433
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2696
    R-Factor(R-Work) 0.2709
    R-Factor(R-Free) 0.2865
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9433
    Shell Resolution(Low) 2.9968
    Number of Reflections(R-Free) 156
    Number of Reflections(R-Work) 2642
    R-Factor(R-Work) 0.27
    R-Factor(R-Free) 0.319
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9968
    Shell Resolution(Low) 3.0544
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2676
    R-Factor(R-Work) 0.2679
    R-Factor(R-Free) 0.3155
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0544
    Shell Resolution(Low) 3.1168
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2629
    R-Factor(R-Work) 0.275
    R-Factor(R-Free) 0.3533
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1168
    Shell Resolution(Low) 3.1845
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 2645
    R-Factor(R-Work) 0.2685
    R-Factor(R-Free) 0.3036
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1845
    Shell Resolution(Low) 3.2586
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.2694
    R-Factor(R-Free) 0.3572
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2586
    Shell Resolution(Low) 3.3401
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2645
    R-Factor(R-Work) 0.2653
    R-Factor(R-Free) 0.2811
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3401
    Shell Resolution(Low) 3.4303
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2683
    R-Factor(R-Work) 0.2465
    R-Factor(R-Free) 0.2999
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4303
    Shell Resolution(Low) 3.5313
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2677
    R-Factor(R-Work) 0.2409
    R-Factor(R-Free) 0.2703
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5313
    Shell Resolution(Low) 3.6452
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2708
    R-Factor(R-Work) 0.2357
    R-Factor(R-Free) 0.3006
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6452
    Shell Resolution(Low) 3.7754
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2658
    R-Factor(R-Work) 0.2339
    R-Factor(R-Free) 0.2647
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7754
    Shell Resolution(Low) 3.9265
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2672
    R-Factor(R-Work) 0.2276
    R-Factor(R-Free) 0.2805
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9265
    Shell Resolution(Low) 4.1052
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2694
    R-Factor(R-Work) 0.2175
    R-Factor(R-Free) 0.2353
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1052
    Shell Resolution(Low) 4.3215
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.2051
    R-Factor(R-Free) 0.2382
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.3215
    Shell Resolution(Low) 4.592
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2694
    R-Factor(R-Work) 0.2001
    R-Factor(R-Free) 0.2579
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.592
    Shell Resolution(Low) 4.9463
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2708
    R-Factor(R-Work) 0.198
    R-Factor(R-Free) 0.213
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9463
    Shell Resolution(Low) 5.4435
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2746
    R-Factor(R-Work) 0.2203
    R-Factor(R-Free) 0.2552
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.4435
    Shell Resolution(Low) 6.2298
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2729
    R-Factor(R-Work) 0.2313
    R-Factor(R-Free) 0.2623
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2298
    Shell Resolution(Low) 7.8438
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 2770
    R-Factor(R-Work) 0.2152
    R-Factor(R-Free) 0.226
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.8438
    Shell Resolution(Low) 49.2002
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 2906
    R-Factor(R-Work) 0.1925
    R-Factor(R-Free) 0.2368
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.074
    f_dihedral_angle_d 17.677
    f_angle_d 1.329
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 16440
    Nucleic Acid Atoms 0
    Heterogen Atoms 372
    Solvent Atoms 381
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution phaser
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8_1069)
    model building phaser
    data collection HKL-2000