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X-RAY DIFFRACTION
Materials and Methods page
3V0N
  •   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, 6-9% PEG-3350 , VAPOR DIFFUSION, HANGING DROP, temperature 295K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 78.2 α = 90
    b = 153.83 β = 90
    c = 52.4 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) 1.75
    Resolution(Low) 30
    Number Reflections(All) 64706
    Number Reflections(Observed) 64658
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.069
    B(Isotropic) From Wilson Plot 26.278
    Redundancy 5.6
     
    High Resolution Shell Details
    Resolution(High) 1.75
    Resolution(Low) 1.8
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.619
    Mean I Over Sigma(Observed) 3.06
    Redundancy 6.0
    Number Unique Reflections(All) 4688
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.75
    Resolution(Low) 29.021
    Cut-off Sigma(F) 2.0
    Number of Reflections(Observed) 64592
    Number of Reflections(R-Free) 2586
    Percent Reflections(Observed) 99.96
    R-Factor(Observed) 0.1582
    R-Work 0.1571
    R-Free 0.1843
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic+tls
    Mean Isotropic B Value 22.1828
    Anisotropic B[1][1] 5.207
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.2905
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -3.9166
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.75
    Shell Resolution(Low) 1.7837
    Number of Reflections(Observed) 3513
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 3372
    R-Factor(R-Work) 0.2315
    R-Factor(R-Free) 0.2597
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7837
    Shell Resolution(Low) 1.8201
    Number of Reflections(Observed) 3554
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3412
    R-Factor(R-Work) 0.2121
    R-Factor(R-Free) 0.2466
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8201
    Shell Resolution(Low) 1.8596
    Number of Reflections(Observed) 3528
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 3387
    R-Factor(R-Work) 0.1942
    R-Factor(R-Free) 0.2358
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8596
    Shell Resolution(Low) 1.9029
    Number of Reflections(Observed) 3531
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 3390
    R-Factor(R-Work) 0.1794
    R-Factor(R-Free) 0.1926
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9029
    Shell Resolution(Low) 1.9505
    Number of Reflections(Observed) 3552
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3409
    R-Factor(R-Work) 0.162
    R-Factor(R-Free) 0.1752
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9505
    Shell Resolution(Low) 2.0032
    Number of Reflections(Observed) 3558
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3416
    R-Factor(R-Work) 0.1521
    R-Factor(R-Free) 0.197
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0032
    Shell Resolution(Low) 2.0621
    Number of Reflections(Observed) 3539
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3397
    R-Factor(R-Work) 0.1507
    R-Factor(R-Free) 0.1791
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0621
    Shell Resolution(Low) 2.1287
    Number of Reflections(Observed) 3552
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3410
    R-Factor(R-Work) 0.1518
    R-Factor(R-Free) 0.1865
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1287
    Shell Resolution(Low) 2.2047
    Number of Reflections(Observed) 3566
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3423
    R-Factor(R-Work) 0.1498
    R-Factor(R-Free) 0.1799
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2047
    Shell Resolution(Low) 2.293
    Number of Reflections(Observed) 3593
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3450
    R-Factor(R-Work) 0.1436
    R-Factor(R-Free) 0.183
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.293
    Shell Resolution(Low) 2.3973
    Number of Reflections(Observed) 3554
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3411
    R-Factor(R-Work) 0.1508
    R-Factor(R-Free) 0.18
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3973
    Shell Resolution(Low) 2.5236
    Number of Reflections(Observed) 3575
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3432
    R-Factor(R-Work) 0.1552
    R-Factor(R-Free) 0.2018
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5236
    Shell Resolution(Low) 2.6816
    Number of Reflections(Observed) 3587
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3444
    R-Factor(R-Work) 0.1513
    R-Factor(R-Free) 0.2055
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6816
    Shell Resolution(Low) 2.8885
    Number of Reflections(Observed) 3616
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3471
    R-Factor(R-Work) 0.163
    R-Factor(R-Free) 0.2059
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8885
    Shell Resolution(Low) 3.1788
    Number of Reflections(Observed) 3598
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 3454
    R-Factor(R-Work) 0.1557
    R-Factor(R-Free) 0.1846
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1788
    Shell Resolution(Low) 3.6381
    Number of Reflections(Observed) 3649
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3503
    R-Factor(R-Work) 0.1479
    R-Factor(R-Free) 0.152
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6381
    Shell Resolution(Low) 4.5807
    Number of Reflections(Observed) 3680
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 3532
    R-Factor(R-Work) 0.1316
    R-Factor(R-Free) 0.1561
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5807
    Shell Resolution(Low) 29.025
    Number of Reflections(Observed) 3847
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 3693
    R-Factor(R-Work) 0.1755
    R-Factor(R-Free) 0.1853
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 16.415
    f_plane_restr 0.007
    f_chiral_restr 0.089
    f_angle_d 1.246
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4720
    Nucleic Acid Atoms 0
    Heterogen Atoms 139
    Solvent Atoms 546
     
     
  •   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