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X-RAY DIFFRACTION
Materials and Methods page
4IBU
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.1
    Temperature 293.0
    Details 1:2 PROTEIN/DNA RATIO, 14% PEG 3350, 0.14M Li-Acetate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 54.54 α = 82.96
    b = 58.16 β = 87.78
    c = 77.97 γ = 73.57
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4
    Details TOROIDAL MIRROR
    Collection Date 2008-02-25
     
    Diffraction Radiation
    Monochromator DIAMOND (111), GE(220)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-2
    Wavelength 0.9330
    Site ESRF
    Beamline ID14-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.69
    Resolution(Low) 40
    Number Reflections(Observed) 96978
    Percent Possible(Observed) 94.7
    R Merge I(Observed) 0.047
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 1.69
    Resolution(Low) 1.72
    Percent Possible(All) 64.4
    R Merge I(Observed) 0.355
    Redundancy 3.7
    Number Unique Reflections(All) 3280
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.7
    Resolution(Low) 30.118
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 1.97
    Number of Reflections(all) 95621
    Number of Reflections(Observed) 95621
    Number of Reflections(R-Free) 4783
    Percent Reflections(Observed) 95.33
    R-Factor(Observed) 0.1645
    R-Work 0.1628
    R-Free 0.1971
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 26.7876
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7
    Shell Resolution(Low) 1.7193
    Number of Reflections(R-Free) 117
    Number of Reflections(R-Work) 2076
    R-Factor(R-Work) 0.2205
    R-Factor(R-Free) 0.2811
    Percent Reflections(Observed) 66.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7193
    Shell Resolution(Low) 1.7396
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2305
    R-Factor(R-Work) 0.2057
    R-Factor(R-Free) 0.2297
    Percent Reflections(Observed) 73.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7396
    Shell Resolution(Low) 1.7608
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2694
    R-Factor(R-Work) 0.2014
    R-Factor(R-Free) 0.2333
    Percent Reflections(Observed) 84.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7608
    Shell Resolution(Low) 1.7831
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2992
    R-Factor(R-Work) 0.2035
    R-Factor(R-Free) 0.2684
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7831
    Shell Resolution(Low) 1.8065
    Number of Reflections(R-Free) 189
    Number of Reflections(R-Work) 3081
    R-Factor(R-Work) 0.1873
    R-Factor(R-Free) 0.2391
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8065
    Shell Resolution(Low) 1.8313
    Number of Reflections(R-Free) 161
    Number of Reflections(R-Work) 3079
    R-Factor(R-Work) 0.1888
    R-Factor(R-Free) 0.2524
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8313
    Shell Resolution(Low) 1.8574
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 3062
    R-Factor(R-Work) 0.1827
    R-Factor(R-Free) 0.2047
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8574
    Shell Resolution(Low) 1.8851
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 3062
    R-Factor(R-Work) 0.1827
    R-Factor(R-Free) 0.2371
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8851
    Shell Resolution(Low) 1.9146
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 3048
    R-Factor(R-Work) 0.1833
    R-Factor(R-Free) 0.2039
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9146
    Shell Resolution(Low) 1.946
    Number of Reflections(R-Free) 177
    Number of Reflections(R-Work) 3171
    R-Factor(R-Work) 0.1863
    R-Factor(R-Free) 0.2602
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.946
    Shell Resolution(Low) 1.9795
    Number of Reflections(R-Free) 178
    Number of Reflections(R-Work) 2988
    R-Factor(R-Work) 0.181
    R-Factor(R-Free) 0.2108
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9795
    Shell Resolution(Low) 2.0155
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 3178
    R-Factor(R-Work) 0.1791
    R-Factor(R-Free) 0.2444
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0155
    Shell Resolution(Low) 2.0543
    Number of Reflections(R-Free) 154
    Number of Reflections(R-Work) 3071
    R-Factor(R-Work) 0.1705
    R-Factor(R-Free) 0.2223
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0543
    Shell Resolution(Low) 2.0962
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 3117
    R-Factor(R-Work) 0.1705
    R-Factor(R-Free) 0.2113
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0962
    Shell Resolution(Low) 2.1418
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 3070
    R-Factor(R-Work) 0.1707
    R-Factor(R-Free) 0.2304
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1418
    Shell Resolution(Low) 2.1916
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3099
    R-Factor(R-Work) 0.1678
    R-Factor(R-Free) 0.1951
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1916
    Shell Resolution(Low) 2.2464
    Number of Reflections(R-Free) 186
    Number of Reflections(R-Work) 3083
    R-Factor(R-Work) 0.1602
    R-Factor(R-Free) 0.2013
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2464
    Shell Resolution(Low) 2.3071
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 3109
    R-Factor(R-Work) 0.1652
    R-Factor(R-Free) 0.2083
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3071
    Shell Resolution(Low) 2.3749
    Number of Reflections(R-Free) 166
    Number of Reflections(R-Work) 3115
    R-Factor(R-Work) 0.1687
    R-Factor(R-Free) 0.2011
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3749
    Shell Resolution(Low) 2.4516
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 3131
    R-Factor(R-Work) 0.1723
    R-Factor(R-Free) 0.2181
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4516
    Shell Resolution(Low) 2.5391
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 3131
    R-Factor(R-Work) 0.1713
    R-Factor(R-Free) 0.2132
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5391
    Shell Resolution(Low) 2.6407
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 3120
    R-Factor(R-Work) 0.1735
    R-Factor(R-Free) 0.2325
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6407
    Shell Resolution(Low) 2.7608
    Number of Reflections(R-Free) 165
    Number of Reflections(R-Work) 3126
    R-Factor(R-Work) 0.1759
    R-Factor(R-Free) 0.2082
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7608
    Shell Resolution(Low) 2.9063
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 3153
    R-Factor(R-Work) 0.178
    R-Factor(R-Free) 0.2271
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9063
    Shell Resolution(Low) 3.0882
    Number of Reflections(R-Free) 157
    Number of Reflections(R-Work) 3137
    R-Factor(R-Work) 0.1725
    R-Factor(R-Free) 0.2027
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0882
    Shell Resolution(Low) 3.3264
    Number of Reflections(R-Free) 195
    Number of Reflections(R-Work) 3095
    R-Factor(R-Work) 0.1636
    R-Factor(R-Free) 0.1944
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3264
    Shell Resolution(Low) 3.6606
    Number of Reflections(R-Free) 160
    Number of Reflections(R-Work) 3166
    R-Factor(R-Work) 0.1428
    R-Factor(R-Free) 0.1686
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6606
    Shell Resolution(Low) 4.1891
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 3152
    R-Factor(R-Work) 0.1423
    R-Factor(R-Free) 0.1659
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.1891
    Shell Resolution(Low) 5.2732
    Number of Reflections(R-Free) 170
    Number of Reflections(R-Work) 3140
    R-Factor(R-Work) 0.1248
    R-Factor(R-Free) 0.1455
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.2732
    Shell Resolution(Low) 30.1228
    Number of Reflections(R-Free) 158
    Number of Reflections(R-Work) 3087
    R-Factor(R-Work) 0.1508
    R-Factor(R-Free) 0.1574
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 17.442
    f_plane_restr 0.006
    f_chiral_restr 0.079
    f_angle_d 1.166
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6119
    Nucleic Acid Atoms 934
    Heterogen Atoms 76
    Solvent Atoms 959
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution MOLREP
    Structure Refinement PHENIX (phenix.refine: 1.8.1_1168)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction HKL