POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4IBS
  •   Crystallization Hide
    Crystallization Experiments
    Method Vapor diffusion, hanging drop
    pH 6.1
    Temperature 293.0
    Details 12% PEG 3350, 0.12M Mg-Formate, pH 6.1, Vapor diffusion, hanging drop, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 68.85 α = 90
    b = 70.18 β = 90
    c = 83.73 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 IMAGE PLATE
    Type RIGAKU RAXIS IV++
    Details BLUE CONFOCAL MIRRORS
    Collection Date 2005-06-06
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RUH3R
    Wavelength List 1.54178
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.78
    Resolution(Low) 32
    Number Reflections(Observed) 74257
    Percent Possible(Observed) 97.1
    R Merge I(Observed) 0.059
    Redundancy 7.3
     
    High Resolution Shell Details
    Resolution(High) 1.78
    Resolution(Low) 1.81
    Percent Possible(All) 83.1
    R Merge I(Observed) 0.335
    Redundancy 5.9
    Number Unique Reflections(All) 3178
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.78
    Resolution(Low) 25.05
    Cut-off Sigma(F) 1.38
    Number of Reflections(all) 74239
    Number of Reflections(Observed) 74239
    Number of Reflections(R-Free) 2564
    Percent Reflections(Observed) 97.06
    R-Factor(Observed) 0.1642
    R-Work 0.1633
    R-Free 0.1807
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 21.0129
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.78
    Shell Resolution(Low) 1.8147
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 3408
    R-Factor(R-Work) 0.2922
    R-Factor(R-Free) 0.3263
    Percent Reflections(Observed) 80.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8147
    Shell Resolution(Low) 1.8517
    Number of Reflections(R-Free) 123
    Number of Reflections(R-Work) 3698
    R-Factor(R-Work) 0.2556
    R-Factor(R-Free) 0.2481
    Percent Reflections(Observed) 88.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8517
    Shell Resolution(Low) 1.8919
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 3868
    R-Factor(R-Work) 0.2209
    R-Factor(R-Free) 0.2167
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8919
    Shell Resolution(Low) 1.9359
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 3931
    R-Factor(R-Work) 0.196
    R-Factor(R-Free) 0.2072
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9359
    Shell Resolution(Low) 1.9842
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 3952
    R-Factor(R-Work) 0.1894
    R-Factor(R-Free) 0.1886
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9842
    Shell Resolution(Low) 2.0378
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 3979
    R-Factor(R-Work) 0.1839
    R-Factor(R-Free) 0.1745
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0378
    Shell Resolution(Low) 2.0977
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 3973
    R-Factor(R-Work) 0.1828
    R-Factor(R-Free) 0.2244
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0977
    Shell Resolution(Low) 2.1654
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 3988
    R-Factor(R-Work) 0.1769
    R-Factor(R-Free) 0.1955
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1654
    Shell Resolution(Low) 2.2426
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 4010
    R-Factor(R-Work) 0.1761
    R-Factor(R-Free) 0.1951
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2426
    Shell Resolution(Low) 2.3323
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 4035
    R-Factor(R-Work) 0.1658
    R-Factor(R-Free) 0.1511
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3323
    Shell Resolution(Low) 2.4382
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 4065
    R-Factor(R-Work) 0.1694
    R-Factor(R-Free) 0.2209
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4382
    Shell Resolution(Low) 2.5665
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 4019
    R-Factor(R-Work) 0.167
    R-Factor(R-Free) 0.2042
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5665
    Shell Resolution(Low) 2.7269
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 4085
    R-Factor(R-Work) 0.163
    R-Factor(R-Free) 0.1631
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7269
    Shell Resolution(Low) 2.9368
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 4072
    R-Factor(R-Work) 0.1596
    R-Factor(R-Free) 0.1715
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9368
    Shell Resolution(Low) 3.2311
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 4112
    R-Factor(R-Work) 0.1594
    R-Factor(R-Free) 0.1822
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2311
    Shell Resolution(Low) 3.6958
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 4127
    R-Factor(R-Work) 0.1475
    R-Factor(R-Free) 0.1566
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.6958
    Shell Resolution(Low) 4.6457
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 4149
    R-Factor(R-Work) 0.1203
    R-Factor(R-Free) 0.154
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.6457
    Shell Resolution(Low) 19.3498
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 4199
    R-Factor(R-Work) 0.145
    R-Factor(R-Free) 0.1648
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 13.796
    f_plane_restr 0.004
    f_chiral_restr 0.058
    f_angle_d 0.877
    f_bond_d 0.004
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5985
    Nucleic Acid Atoms 0
    Heterogen Atoms 8
    Solvent Atoms 649
     
     
  •   Software and Computing Hide
    Computing
    Data Collection StructureStudio
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: dev_1218)
     
    Software
    data extraction pdb_extract version: 3.11
    refinement phenix
    molecular replacement Phaser
    data reduction HKL