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X-RAY DIFFRACTION
Materials and Methods page
4MRP
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    pH 5.4
    Temperature 277.0
    Details 100 mM sodium citrate pH 5.4, 200 mM magnesium acetate, and 12% w/v polyethylene glycol 5,000 mono methyl ether, VAPOR DIFFUSION, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 321.85 α = 90
    b = 95.26 β = 102.01
    c = 79.01 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2013-06-05
     
    Diffraction Radiation
    Monochromator Liquid nitrogen-cooled double crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL12-2
    Wavelength List 0.9762
    Site SSRL
    Beamline BL12-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.5
    Resolution(Low) 40
    Number Reflections(Observed) 79820
    Percent Possible(Observed) 98.7
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.5
    Resolution(Low) 39.736
    Cut-off Sigma(F) 1.33
    Number of Reflections(Observed) 79384
    Number of Reflections(R-Free) 3959
    Percent Reflections(Observed) 98.05
    R-Factor(Observed) 0.2035
    R-Work 0.2021
    R-Free 0.2309
    R-Free Selection Details PHENIX
     
    Temperature Factor Modeling
    Data Not Available
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5
    Shell Resolution(Low) 2.5305
    Number of Reflections(Observed) 2546
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2546
    R-Factor(R-Work) 0.4664
    R-Factor(R-Free) 0.4581
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5305
    Shell Resolution(Low) 2.5625
    Number of Reflections(Observed) 2664
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2664
    R-Factor(R-Work) 0.4231
    R-Factor(R-Free) 0.4705
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5625
    Shell Resolution(Low) 2.5963
    Number of Reflections(Observed) 2646
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2646
    R-Factor(R-Work) 0.3853
    R-Factor(R-Free) 0.4037
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5963
    Shell Resolution(Low) 2.6318
    Number of Reflections(Observed) 2697
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2697
    R-Factor(R-Work) 0.3616
    R-Factor(R-Free) 0.3968
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6318
    Shell Resolution(Low) 2.6694
    Number of Reflections(Observed) 2616
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.3462
    R-Factor(R-Free) 0.3781
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6694
    Shell Resolution(Low) 2.7092
    Number of Reflections(Observed) 2712
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 2712
    R-Factor(R-Work) 0.32
    R-Factor(R-Free) 0.34
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7092
    Shell Resolution(Low) 2.7516
    Number of Reflections(Observed) 2713
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2713
    R-Factor(R-Work) 0.3023
    R-Factor(R-Free) 0.3177
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7516
    Shell Resolution(Low) 2.7967
    Number of Reflections(Observed) 2630
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2630
    R-Factor(R-Work) 0.2982
    R-Factor(R-Free) 0.3379
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7967
    Shell Resolution(Low) 2.8449
    Number of Reflections(Observed) 2630
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2630
    R-Factor(R-Work) 0.2994
    R-Factor(R-Free) 0.3612
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8449
    Shell Resolution(Low) 2.8966
    Number of Reflections(Observed) 2701
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 2701
    R-Factor(R-Work) 0.2729
    R-Factor(R-Free) 0.3331
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8966
    Shell Resolution(Low) 2.9523
    Number of Reflections(Observed) 2725
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2725
    R-Factor(R-Work) 0.2632
    R-Factor(R-Free) 0.2977
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9523
    Shell Resolution(Low) 3.0125
    Number of Reflections(Observed) 2690
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2690
    R-Factor(R-Work) 0.2498
    R-Factor(R-Free) 0.2786
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0125
    Shell Resolution(Low) 3.078
    Number of Reflections(Observed) 2751
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2751
    R-Factor(R-Work) 0.258
    R-Factor(R-Free) 0.3248
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.078
    Shell Resolution(Low) 3.1496
    Number of Reflections(Observed) 2686
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2686
    R-Factor(R-Work) 0.2523
    R-Factor(R-Free) 0.305
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1496
    Shell Resolution(Low) 3.2283
    Number of Reflections(Observed) 2700
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2700
    R-Factor(R-Work) 0.2493
    R-Factor(R-Free) 0.2587
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2283
    Shell Resolution(Low) 3.3156
    Number of Reflections(Observed) 2676
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2676
    R-Factor(R-Work) 0.2226
    R-Factor(R-Free) 0.2747
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3156
    Shell Resolution(Low) 3.4131
    Number of Reflections(Observed) 2699
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2699
    R-Factor(R-Work) 0.2076
    R-Factor(R-Free) 0.2522
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4131
    Shell Resolution(Low) 3.5232
    Number of Reflections(Observed) 2626
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2626
    R-Factor(R-Work) 0.2032
    R-Factor(R-Free) 0.2303
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5232
    Shell Resolution(Low) 3.649
    Number of Reflections(Observed) 2732
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 2732
    R-Factor(R-Work) 0.1875
    R-Factor(R-Free) 0.2219
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.649
    Shell Resolution(Low) 3.795
    Number of Reflections(Observed) 2725
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2725
    R-Factor(R-Work) 0.1709
    R-Factor(R-Free) 0.2253
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.795
    Shell Resolution(Low) 3.9676
    Number of Reflections(Observed) 2764
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2764
    R-Factor(R-Work) 0.1657
    R-Factor(R-Free) 0.1933
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9676
    Shell Resolution(Low) 4.1765
    Number of Reflections(Observed) 2719
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2719
    R-Factor(R-Work) 0.1658
    R-Factor(R-Free) 0.222
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1765
    Shell Resolution(Low) 4.4379
    Number of Reflections(Observed) 2661
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2661
    R-Factor(R-Work) 0.1597
    R-Factor(R-Free) 0.2076
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4379
    Shell Resolution(Low) 4.78
    Number of Reflections(Observed) 2678
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2678
    R-Factor(R-Work) 0.1538
    R-Factor(R-Free) 0.1811
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.78
    Shell Resolution(Low) 5.2601
    Number of Reflections(Observed) 2761
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2761
    R-Factor(R-Work) 0.1515
    R-Factor(R-Free) 0.152
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2601
    Shell Resolution(Low) 6.019
    Number of Reflections(Observed) 2762
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2762
    R-Factor(R-Work) 0.1851
    R-Factor(R-Free) 0.198
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.019
    Shell Resolution(Low) 7.5747
    Number of Reflections(Observed) 2707
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2707
    R-Factor(R-Work) 0.1967
    R-Factor(R-Free) 0.1946
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 7.5747
    Shell Resolution(Low) 39.7411
    Number of Reflections(Observed) 2808
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2808
    R-Factor(R-Work) 0.1816
    R-Factor(R-Free) 0.2053
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.007
    f_chiral_restr 0.076
    f_dihedral_angle_d 14.76
    f_angle_d 1.222
    f_bond_d 0.009
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 9303
    Nucleic Acid Atoms 0
    Heterogen Atoms 124
    Solvent Atoms 246
     
     
  •   Software and Computing Hide
    Computing
    Data Collection BLU-ICE
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) AIMLESS
    Structure Solution REFMAC5 (rigid body)
    Structure Refinement PHENIX (phenix.refine: 1.8.2_1309)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8.2_1309)
    model building REFMAC5 version: (rigid body)
    data collection BLU-ICE