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X-RAY DIFFRACTION
Materials and Methods page
4M9L
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 7.5
    Temperature 291.0
    Details 14% PEG 3350, 300 mM sodium acetate pH 9, 50 mM HEPES pH 7.5, vapor diffusion, hanging drop, temperature 291K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 54.36 α = 90
    b = 80.2 β = 108.59
    c = 54.6 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 104
     
    Diffraction Detector
    Detector IMAGE PLATE
    Type MAR scanner 345 mm plate
    Details mirrors
    Collection Date 2013-05-14
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RUH3R
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.09
    Resolution(Low) 14
    Percent Possible(Observed) 96.5
    R Merge I(Observed) 0.08
    B(Isotropic) From Wilson Plot 30.21
    Redundancy 8.8
     
    High Resolution Shell Details
    Resolution(High) 2.091
    Resolution(Low) 2.16
    Percent Possible(All) 91.4
    R Merge I(Observed) 0.612
    Redundancy 4.2
    Number Unique Reflections(All) 2378
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.091
    Resolution(Low) 13.84
    Cut-off Sigma(F) 1.34
    Number of Reflections(Observed) 49217
    Number of Reflections(R-Free) 4922
    Percent Reflections(Observed) 95.52
    R-Factor(Observed) 0.1929
    R-Work 0.1887
    R-Free 0.2307
     
    Temperature Factor Modeling
    Mean Isotropic B Value 42.3093
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0907
    Shell Resolution(Low) 2.1144
    Number of Reflections(R-Free) 174
    Number of Reflections(R-Work) 1216
    R-Factor(R-Work) 0.3098
    R-Factor(R-Free) 0.3753
    Percent Reflections(Observed) 81.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1144
    Shell Resolution(Low) 2.1391
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 1283
    R-Factor(R-Work) 0.2867
    R-Factor(R-Free) 0.326
    Percent Reflections(Observed) 86.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1391
    Shell Resolution(Low) 2.1651
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 1373
    R-Factor(R-Work) 0.2707
    R-Factor(R-Free) 0.3056
    Percent Reflections(Observed) 87.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1651
    Shell Resolution(Low) 2.1924
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 1447
    R-Factor(R-Work) 0.2627
    R-Factor(R-Free) 0.2834
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1924
    Shell Resolution(Low) 2.2212
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 1397
    R-Factor(R-Work) 0.2725
    R-Factor(R-Free) 0.3292
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2212
    Shell Resolution(Low) 2.2515
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 1515
    R-Factor(R-Work) 0.2608
    R-Factor(R-Free) 0.3077
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2515
    Shell Resolution(Low) 2.2835
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 1457
    R-Factor(R-Work) 0.2564
    R-Factor(R-Free) 0.3173
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2835
    Shell Resolution(Low) 2.3174
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 1460
    R-Factor(R-Work) 0.2384
    R-Factor(R-Free) 0.2602
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3174
    Shell Resolution(Low) 2.3535
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 1461
    R-Factor(R-Work) 0.2279
    R-Factor(R-Free) 0.2648
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3535
    Shell Resolution(Low) 2.3919
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 1483
    R-Factor(R-Work) 0.2298
    R-Factor(R-Free) 0.2881
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3919
    Shell Resolution(Low) 2.4329
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 1502
    R-Factor(R-Work) 0.23
    R-Factor(R-Free) 0.3243
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4329
    Shell Resolution(Low) 2.4769
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 1497
    R-Factor(R-Work) 0.2279
    R-Factor(R-Free) 0.2573
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4769
    Shell Resolution(Low) 2.5242
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1474
    R-Factor(R-Work) 0.2339
    R-Factor(R-Free) 0.277
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5242
    Shell Resolution(Low) 2.5754
    Number of Reflections(R-Free) 162
    Number of Reflections(R-Work) 1498
    R-Factor(R-Work) 0.2172
    R-Factor(R-Free) 0.2692
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5754
    Shell Resolution(Low) 2.6311
    Number of Reflections(R-Free) 173
    Number of Reflections(R-Work) 1485
    R-Factor(R-Work) 0.2177
    R-Factor(R-Free) 0.2713
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6311
    Shell Resolution(Low) 2.6918
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 1528
    R-Factor(R-Work) 0.2099
    R-Factor(R-Free) 0.2709
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6918
    Shell Resolution(Low) 2.7586
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 1464
    R-Factor(R-Work) 0.204
    R-Factor(R-Free) 0.2533
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7586
    Shell Resolution(Low) 2.8326
    Number of Reflections(R-Free) 185
    Number of Reflections(R-Work) 1481
    R-Factor(R-Work) 0.1963
    R-Factor(R-Free) 0.2106
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8326
    Shell Resolution(Low) 2.9152
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 1523
    R-Factor(R-Work) 0.2058
    R-Factor(R-Free) 0.2586
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9152
    Shell Resolution(Low) 3.0084
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 1578
    R-Factor(R-Work) 0.2032
    R-Factor(R-Free) 0.2532
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0084
    Shell Resolution(Low) 3.1147
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 1449
    R-Factor(R-Work) 0.197
    R-Factor(R-Free) 0.2921
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1147
    Shell Resolution(Low) 3.2379
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 1547
    R-Factor(R-Work) 0.1873
    R-Factor(R-Free) 0.2489
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2379
    Shell Resolution(Low) 3.3832
    Number of Reflections(R-Free) 175
    Number of Reflections(R-Work) 1503
    R-Factor(R-Work) 0.1778
    R-Factor(R-Free) 0.2333
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3832
    Shell Resolution(Low) 3.5587
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 1511
    R-Factor(R-Work) 0.1616
    R-Factor(R-Free) 0.2004
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5587
    Shell Resolution(Low) 3.7774
    Number of Reflections(R-Free) 172
    Number of Reflections(R-Work) 1531
    R-Factor(R-Work) 0.1644
    R-Factor(R-Free) 0.1873
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7774
    Shell Resolution(Low) 4.0622
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 1510
    R-Factor(R-Work) 0.1528
    R-Factor(R-Free) 0.2009
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.0622
    Shell Resolution(Low) 4.4586
    Number of Reflections(R-Free) 168
    Number of Reflections(R-Work) 1540
    R-Factor(R-Work) 0.1428
    R-Factor(R-Free) 0.165
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.4586
    Shell Resolution(Low) 5.0757
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 1526
    R-Factor(R-Work) 0.1481
    R-Factor(R-Free) 0.184
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.0757
    Shell Resolution(Low) 6.2932
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 1544
    R-Factor(R-Work) 0.1625
    R-Factor(R-Free) 0.2127
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.2932
    Shell Resolution(Low) 13.8407
    Number of Reflections(R-Free) 203
    Number of Reflections(R-Work) 1512
    R-Factor(R-Work) 0.157
    R-Factor(R-Free) 0.171
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 18.591
    f_plane_restr 0.002
    f_chiral_restr 0.038
    f_angle_d 0.718
    f_bond_d 0.003
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2444
    Nucleic Acid Atoms 627
    Heterogen Atoms 32
    Solvent Atoms 314
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser version: 2.5.1
    data reduction SCALEPACK
    data collection DENZO