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X-RAY DIFFRACTION
Materials and Methods page
3V0M
  •   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 = 78.17 α = 90
    b = 153.25 β = 90
    c = 52.72 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) 1.68
    Resolution(Low) 30
    Number Reflections(All) 73143
    Number Reflections(Observed) 70045
    Percent Possible(Observed) 95.8
    R Merge I(Observed) 0.067
    B(Isotropic) From Wilson Plot 25.996
    Redundancy 5.9
     
    High Resolution Shell Details
    Resolution(High) 1.68
    Resolution(Low) 1.72
    Percent Possible(All) 90.3
    R Merge I(Observed) 0.688
    Mean I Over Sigma(Observed) 2.23
    Redundancy 4.8
    Number Unique Reflections(All) 5325
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.68
    Resolution(Low) 29.053
    Cut-off Sigma(F) 1.99
    Number of Reflections(Observed) 69982
    Number of Reflections(R-Free) 2799
    Percent Reflections(Observed) 95.8
    R-Factor(Observed) 0.1649
    R-Work 0.1638
    R-Free 0.1918
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic+tls
    Mean Isotropic B Value 21.9192
    Anisotropic B[1][1] 2.0355
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -2.2067
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.1712
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.68
    Shell Resolution(Low) 1.709
    Number of Reflections(Observed) 3239
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 3110
    R-Factor(R-Work) 0.2811
    R-Factor(R-Free) 0.2956
    Percent Reflections(Observed) 90.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.709
    Shell Resolution(Low) 1.74
    Number of Reflections(Observed) 3299
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 3167
    R-Factor(R-Work) 0.249
    R-Factor(R-Free) 0.2822
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.74
    Shell Resolution(Low) 1.7735
    Number of Reflections(Observed) 3328
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 3194
    R-Factor(R-Work) 0.2297
    R-Factor(R-Free) 0.227
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7735
    Shell Resolution(Low) 1.8097
    Number of Reflections(Observed) 3351
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 3217
    R-Factor(R-Work) 0.2132
    R-Factor(R-Free) 0.2585
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8097
    Shell Resolution(Low) 1.849
    Number of Reflections(Observed) 3403
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 3267
    R-Factor(R-Work) 0.207
    R-Factor(R-Free) 0.2667
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.849
    Shell Resolution(Low) 1.892
    Number of Reflections(Observed) 3405
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 3269
    R-Factor(R-Work) 0.1823
    R-Factor(R-Free) 0.2469
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.892
    Shell Resolution(Low) 1.9394
    Number of Reflections(Observed) 3413
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 3276
    R-Factor(R-Work) 0.1626
    R-Factor(R-Free) 0.1804
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9394
    Shell Resolution(Low) 1.9918
    Number of Reflections(Observed) 3453
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 3315
    R-Factor(R-Work) 0.152
    R-Factor(R-Free) 0.1932
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9918
    Shell Resolution(Low) 2.0504
    Number of Reflections(Observed) 3498
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 3358
    R-Factor(R-Work) 0.1485
    R-Factor(R-Free) 0.1727
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0504
    Shell Resolution(Low) 2.1165
    Number of Reflections(Observed) 3468
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 3329
    R-Factor(R-Work) 0.1541
    R-Factor(R-Free) 0.2228
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1165
    Shell Resolution(Low) 2.1922
    Number of Reflections(Observed) 3497
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 3358
    R-Factor(R-Work) 0.1578
    R-Factor(R-Free) 0.1852
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1922
    Shell Resolution(Low) 2.2799
    Number of Reflections(Observed) 3499
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 3360
    R-Factor(R-Work) 0.1527
    R-Factor(R-Free) 0.2129
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2799
    Shell Resolution(Low) 2.3836
    Number of Reflections(Observed) 3566
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3423
    R-Factor(R-Work) 0.154
    R-Factor(R-Free) 0.1952
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3836
    Shell Resolution(Low) 2.5092
    Number of Reflections(Observed) 3545
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 3403
    R-Factor(R-Work) 0.1561
    R-Factor(R-Free) 0.2186
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5092
    Shell Resolution(Low) 2.6663
    Number of Reflections(Observed) 3576
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3433
    R-Factor(R-Work) 0.1536
    R-Factor(R-Free) 0.1858
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6663
    Shell Resolution(Low) 2.872
    Number of Reflections(Observed) 3617
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3472
    R-Factor(R-Work) 0.1594
    R-Factor(R-Free) 0.2145
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.872
    Shell Resolution(Low) 3.1607
    Number of Reflections(Observed) 3612
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3467
    R-Factor(R-Work) 0.1589
    R-Factor(R-Free) 0.1769
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1607
    Shell Resolution(Low) 3.6174
    Number of Reflections(Observed) 3652
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 3506
    R-Factor(R-Work) 0.1519
    R-Factor(R-Free) 0.1811
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6174
    Shell Resolution(Low) 4.5547
    Number of Reflections(Observed) 3694
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 3547
    R-Factor(R-Work) 0.1382
    R-Factor(R-Free) 0.1381
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.5547
    Shell Resolution(Low) 29.0575
    Number of Reflections(Observed) 3867
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 3712
    R-Factor(R-Work) 0.1807
    R-Factor(R-Free) 0.1852
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.34
    f_plane_restr 0.007
    f_chiral_restr 0.09
    f_angle_d 1.3
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4712
    Nucleic Acid Atoms 0
    Heterogen Atoms 129
    Solvent Atoms 542
     
     
  •   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