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X-RAY DIFFRACTION
Materials and Methods page
4IBY
  •   Crystallization Hide
    Crystallization Experiments
    Method Vapor diffusion, hanging drop
    pH 6.1
    Temperature 293.0
    Details 20% PEG 3350, 0.2M Na2HPO4, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 43.52 α = 90
    b = 69.21 β = 96.61
    c = 67.19 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 4r
    Details TOROIDAL MIRROR
    Collection Date 2006-04-27
     
    Diffraction Radiation
    Monochromator DIAMOND (111), GE(220)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-3
    Wavelength List 0.9310
    Site ESRF
    Beamline ID14-3
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.45
    Resolution(Low) 25
    Number Reflections(Observed) 69956
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.077
    Redundancy 4.2
     
    High Resolution Shell Details
    Resolution(High) 1.45
    Resolution(Low) 1.47
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.537
    Redundancy 4.1
    Number Unique Reflections(All) 3472
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.45
    Resolution(Low) 21.779
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 1.89
    Number of Reflections(all) 69847
    Number of Reflections(Observed) 69847
    Number of Reflections(R-Free) 3524
    Percent Reflections(Observed) 99.49
    R-Factor(Observed) 0.171
    R-Work 0.1694
    R-Free 0.2003
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 14.5475
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.45
    Shell Resolution(Low) 1.4694
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2598
    R-Factor(R-Work) 0.2367
    R-Factor(R-Free) 0.265
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4694
    Shell Resolution(Low) 1.4904
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2680
    R-Factor(R-Work) 0.2287
    R-Factor(R-Free) 0.2592
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4904
    Shell Resolution(Low) 1.5126
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.2162
    R-Factor(R-Free) 0.2377
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5126
    Shell Resolution(Low) 1.5363
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2649
    R-Factor(R-Work) 0.1992
    R-Factor(R-Free) 0.2343
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5363
    Shell Resolution(Low) 1.5614
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2628
    R-Factor(R-Work) 0.1985
    R-Factor(R-Free) 0.2387
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5614
    Shell Resolution(Low) 1.5884
    Number of Reflections(R-Free) 164
    Number of Reflections(R-Work) 2644
    R-Factor(R-Work) 0.1866
    R-Factor(R-Free) 0.2241
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5884
    Shell Resolution(Low) 1.6172
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2656
    R-Factor(R-Work) 0.1855
    R-Factor(R-Free) 0.209
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6172
    Shell Resolution(Low) 1.6483
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2661
    R-Factor(R-Work) 0.1806
    R-Factor(R-Free) 0.2162
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6483
    Shell Resolution(Low) 1.682
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2684
    R-Factor(R-Work) 0.1772
    R-Factor(R-Free) 0.2155
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.682
    Shell Resolution(Low) 1.7185
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2622
    R-Factor(R-Work) 0.1712
    R-Factor(R-Free) 0.2186
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7185
    Shell Resolution(Low) 1.7585
    Number of Reflections(R-Free) 159
    Number of Reflections(R-Work) 2621
    R-Factor(R-Work) 0.1732
    R-Factor(R-Free) 0.2114
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7585
    Shell Resolution(Low) 1.8024
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2651
    R-Factor(R-Work) 0.1699
    R-Factor(R-Free) 0.2186
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8024
    Shell Resolution(Low) 1.8511
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2638
    R-Factor(R-Work) 0.1748
    R-Factor(R-Free) 0.1994
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8511
    Shell Resolution(Low) 1.9056
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2632
    R-Factor(R-Work) 0.1891
    R-Factor(R-Free) 0.2001
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9056
    Shell Resolution(Low) 1.967
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.1999
    R-Factor(R-Free) 0.2983
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.967
    Shell Resolution(Low) 2.0373
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2664
    R-Factor(R-Work) 0.1645
    R-Factor(R-Free) 0.2159
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0373
    Shell Resolution(Low) 2.1188
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2610
    R-Factor(R-Work) 0.1645
    R-Factor(R-Free) 0.1983
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1188
    Shell Resolution(Low) 2.2151
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2666
    R-Factor(R-Work) 0.1744
    R-Factor(R-Free) 0.2282
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2151
    Shell Resolution(Low) 2.3318
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2640
    R-Factor(R-Work) 0.1786
    R-Factor(R-Free) 0.2127
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3318
    Shell Resolution(Low) 2.4777
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2679
    R-Factor(R-Work) 0.1627
    R-Factor(R-Free) 0.1935
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4777
    Shell Resolution(Low) 2.6687
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2653
    R-Factor(R-Work) 0.1636
    R-Factor(R-Free) 0.2051
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6687
    Shell Resolution(Low) 2.9367
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2696
    R-Factor(R-Work) 0.1673
    R-Factor(R-Free) 0.1955
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9367
    Shell Resolution(Low) 3.3603
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2679
    R-Factor(R-Work) 0.1582
    R-Factor(R-Free) 0.1837
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3603
    Shell Resolution(Low) 4.2285
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2621
    R-Factor(R-Work) 0.1332
    R-Factor(R-Free) 0.1436
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.2285
    Shell Resolution(Low) 21.7816
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2723
    R-Factor(R-Work) 0.1498
    R-Factor(R-Free) 0.1521
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 12.873
    f_plane_restr 0.005
    f_chiral_restr 0.076
    f_angle_d 1.13
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3077
    Nucleic Acid Atoms 0
    Heterogen Atoms 30
    Solvent Atoms 753
     
     
  •   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
    data reduction HKL