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X-RAY DIFFRACTION
Materials and Methods page
4FQQ
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion
    pH 7
    Temperature 298.0
    Details PEG 3350, sodium malonate, MnCl2, pH 7.0, vapor diffusion, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 54.93 α = 90
    b = 344.74 β = 91.95
    c = 55.23 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 PIXEL
    Type DECTRIS PILATUS 6M
    Collection Date 2012-03-09
     
    Diffraction Radiation
    Monochromator LIQUID NITROGEN-COOLED DOUBLE CRYSTAL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SSRL BEAMLINE BL12-2
    Wavelength List 1.033
    Site SSRL
    Beamline BL12-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.42
    Resolution(Low) 38.31
    Number Reflections(All) 74318
    Number Reflections(Observed) 74318
    Percent Possible(Observed) 95.5
    Redundancy 3.1
     
    High Resolution Shell Details
    Resolution(High) 2.42
    Resolution(Low) 2.55
    Percent Possible(All) 80.1
    R Merge I(Observed) 0.482
    Mean I Over Sigma(Observed) 1.6
    R-Sym I(Observed) 0.482
    Redundancy 2.6
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.42
    Resolution(Low) 37.44
    Cut-off Sigma(F) 1.36
    Number of Reflections(all) 77751
    Number of Reflections(Observed) 74237
    Number of Reflections(R-Free) 1992
    Percent Reflections(Observed) 95.5
    R-Factor(Observed) 0.195
    R-Work 0.194
    R-Free 0.237
     
    Temperature Factor Modeling
    Mean Isotropic B Value 48.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4188
    Shell Resolution(Low) 2.4793
    Number of Reflections(R-Free) 95
    Number of Reflections(R-Work) 3474
    R-Factor(R-Work) 0.2966
    R-Factor(R-Free) 0.3562
    Percent Reflections(Observed) 64.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4793
    Shell Resolution(Low) 2.5463
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 5131
    R-Factor(R-Work) 0.2842
    R-Factor(R-Free) 0.3558
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5463
    Shell Resolution(Low) 2.6213
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 5382
    R-Factor(R-Work) 0.2653
    R-Factor(R-Free) 0.3267
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6213
    Shell Resolution(Low) 2.7058
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 5290
    R-Factor(R-Work) 0.2579
    R-Factor(R-Free) 0.3139
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7058
    Shell Resolution(Low) 2.8025
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 5282
    R-Factor(R-Work) 0.2497
    R-Factor(R-Free) 0.2915
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8025
    Shell Resolution(Low) 2.9147
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 5418
    R-Factor(R-Work) 0.2446
    R-Factor(R-Free) 0.3032
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9147
    Shell Resolution(Low) 3.0473
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 5306
    R-Factor(R-Work) 0.2424
    R-Factor(R-Free) 0.3107
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0473
    Shell Resolution(Low) 3.2079
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 5278
    R-Factor(R-Work) 0.2251
    R-Factor(R-Free) 0.3196
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2079
    Shell Resolution(Low) 3.4087
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 5259
    R-Factor(R-Work) 0.2104
    R-Factor(R-Free) 0.2799
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4087
    Shell Resolution(Low) 3.6717
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 5287
    R-Factor(R-Work) 0.1937
    R-Factor(R-Free) 0.2467
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6717
    Shell Resolution(Low) 4.0408
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 5285
    R-Factor(R-Work) 0.1705
    R-Factor(R-Free) 0.2141
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0408
    Shell Resolution(Low) 4.6246
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 5320
    R-Factor(R-Work) 0.1396
    R-Factor(R-Free) 0.1752
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6246
    Shell Resolution(Low) 5.823
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 5256
    R-Factor(R-Work) 0.1437
    R-Factor(R-Free) 0.1472
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.823
    Shell Resolution(Low) 37.4482
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 5277
    R-Factor(R-Work) 0.1769
    R-Factor(R-Free) 0.2028
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.067
    f_dihedral_angle_d 12.916
    f_angle_d 0.951
    f_bond_d 0.005
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 13261
    Nucleic Acid Atoms 0
    Heterogen Atoms 2
    Solvent Atoms 490
     
     
  •   Software and Computing Hide
    Computing
    Data Collection XDS
    Data Reduction (intensity integration) XSCALE
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (PHENIX.REFINE: 1.8_1069)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    data reduction SCALA version: 3.3.16