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X-RAY DIFFRACTION
Materials and Methods page
3V0P
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 295.0
    Details 50 mM MOPS pH 7, 50-200 mM AMMONIUM SULFATE, 50 mM MnCl2, AND 6-9% PEG-3350 , VAPOR DIFFUSION, HANGING DROP, temperature 295K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 78.3 α = 90
    b = 153.52 β = 90
    c = 52.83 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 MAR CCD 165 mm
    Details Multilayer mirror, curved to focus in the vertical (R = 400 m)
    Collection Date 2010-03-26
     
    Diffraction Radiation
    Monochromator Bent Si (111) crystal, horizontally focusing
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type MAX II BEAMLINE I911-2
    Wavelength List 1.03796
    Site MAX II
    Beamline I911-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.9
    Resolution(Low) 30
    Number Reflections(All) 51152
    Number Reflections(Observed) 49866
    Percent Possible(Observed) 97.5
    R Merge I(Observed) 0.121
    B(Isotropic) From Wilson Plot 22.329
    Redundancy 6.0
     
    High Resolution Shell Details
    Resolution(High) 1.9
    Resolution(Low) 1.95
    Percent Possible(All) 95.5
    R Merge I(Observed) 0.652
    Mean I Over Sigma(Observed) 2.73
    Redundancy 5.2
    Number Unique Reflections(All) 3707
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.9
    Resolution(Low) 29.106
    Cut-off Sigma(F) 2.0
    Number of Reflections(Observed) 49808
    Number of Reflections(R-Free) 1987
    Percent Reflections(Observed) 97.53
    R-Factor(Observed) 0.1606
    R-Work 0.1593
    R-Free 0.1932
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic+tls
    Mean Isotropic B Value 18.1009
    Anisotropic B[1][1] 1.0835
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.5926
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.5092
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9
    Shell Resolution(Low) 1.9475
    Number of Reflections(Observed) 3424
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 3288
    R-Factor(R-Work) 0.1986
    R-Factor(R-Free) 0.2409
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9475
    Shell Resolution(Low) 2.0001
    Number of Reflections(Observed) 3445
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 3308
    R-Factor(R-Work) 0.1838
    R-Factor(R-Free) 0.2257
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0001
    Shell Resolution(Low) 2.059
    Number of Reflections(Observed) 3485
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 3346
    R-Factor(R-Work) 0.1736
    R-Factor(R-Free) 0.2185
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.059
    Shell Resolution(Low) 2.1254
    Number of Reflections(Observed) 3476
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 3337
    R-Factor(R-Work) 0.1687
    R-Factor(R-Free) 0.2106
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1254
    Shell Resolution(Low) 2.2014
    Number of Reflections(Observed) 3491
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 3351
    R-Factor(R-Work) 0.1568
    R-Factor(R-Free) 0.2196
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2014
    Shell Resolution(Low) 2.2895
    Number of Reflections(Observed) 3513
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 3372
    R-Factor(R-Work) 0.1524
    R-Factor(R-Free) 0.1955
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2895
    Shell Resolution(Low) 2.3936
    Number of Reflections(Observed) 3534
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 3395
    R-Factor(R-Work) 0.1526
    R-Factor(R-Free) 0.1993
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3936
    Shell Resolution(Low) 2.5198
    Number of Reflections(Observed) 3536
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3394
    R-Factor(R-Work) 0.1614
    R-Factor(R-Free) 0.2033
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5198
    Shell Resolution(Low) 2.6775
    Number of Reflections(Observed) 3560
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3418
    R-Factor(R-Work) 0.1542
    R-Factor(R-Free) 0.1748
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6775
    Shell Resolution(Low) 2.8841
    Number of Reflections(Observed) 3595
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 3451
    R-Factor(R-Work) 0.1594
    R-Factor(R-Free) 0.219
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8841
    Shell Resolution(Low) 3.174
    Number of Reflections(Observed) 3582
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3439
    R-Factor(R-Work) 0.1594
    R-Factor(R-Free) 0.1836
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.174
    Shell Resolution(Low) 3.6326
    Number of Reflections(Observed) 3632
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 3488
    R-Factor(R-Work) 0.1534
    R-Factor(R-Free) 0.18
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6326
    Shell Resolution(Low) 4.5738
    Number of Reflections(Observed) 3675
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 3528
    R-Factor(R-Work) 0.1373
    R-Factor(R-Free) 0.1685
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5738
    Shell Resolution(Low) 29.109
    Number of Reflections(Observed) 3860
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 3706
    R-Factor(R-Work) 0.171
    R-Factor(R-Free) 0.1819
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 14.811
    f_plane_restr 0.005
    f_chiral_restr 0.073
    f_angle_d 1.049
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4796
    Nucleic Acid Atoms 0
    Heterogen Atoms 131
    Solvent Atoms 568
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MARCCD
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.1_743)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    molecular replacement Phaser version: 2.1.4
    data reduction Xscale