POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4INA
  •   Crystallization Hide
    Crystallization Experiments
    Method Microbatch crystallization under oil
    pH 6.5
    Temperature 277.0
    Details 20% PEG MME 5000, 0.1M BIS-TRIS, pH 6.5, Microbatch crystallization under oil, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 44.64 α = 90
    b = 95.49 β = 101.8
    c = 104.43 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 315
    Collection Date 2012-12-19
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 24-ID-E
    Wavelength List 0.97923
    Site APS
    Beamline 24-ID-E
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.49
    Resolution(Low) 50
    Number Reflections(All) 59291
    Number Reflections(Observed) 57476
    Percent Possible(Observed) 96.9
    R Merge I(Observed) 0.087
    B(Isotropic) From Wilson Plot 35.49
    Redundancy 3.7
     
    High Resolution Shell Details
    Resolution(High) 2.49
    Resolution(Low) 2.6
    Percent Possible(All) 97.7
    R Merge I(Observed) 0.474
    Mean I Over Sigma(Observed) 2.6
    Redundancy 3.7
    Number Unique Reflections(All) 7303
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.488
    Resolution(Low) 45.061
    Cut-off Sigma(F) 0.98
    Number of Reflections(Observed) 57460
    Number of Reflections(R-Free) 2909
    Percent Reflections(Observed) 96.98
    R-Factor(Observed) 0.195
    R-Work 0.193
    R-Free 0.222
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 36.404
    Anisotropic B[1][1] 1.298
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -3.636
    Anisotropic B[2][2] -5.121
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 3.824
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.488
    Shell Resolution(Low) 2.528
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2544
    R-Factor(R-Work) 0.349
    R-Factor(R-Free) 0.377
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.528
    Shell Resolution(Low) 2.572
    Number of Reflections(R-Free) 112
    Number of Reflections(R-Work) 2660
    R-Factor(R-Work) 0.345
    R-Factor(R-Free) 0.4
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.572
    Shell Resolution(Low) 2.619
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2720
    R-Factor(R-Work) 0.332
    R-Factor(R-Free) 0.364
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.619
    Shell Resolution(Low) 2.669
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2590
    R-Factor(R-Work) 0.298
    R-Factor(R-Free) 0.354
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.669
    Shell Resolution(Low) 2.724
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.284
    R-Factor(R-Free) 0.332
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.724
    Shell Resolution(Low) 2.783
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.271
    R-Factor(R-Free) 0.253
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.783
    Shell Resolution(Low) 2.848
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2615
    R-Factor(R-Work) 0.248
    R-Factor(R-Free) 0.308
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.848
    Shell Resolution(Low) 2.919
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2620
    R-Factor(R-Work) 0.237
    R-Factor(R-Free) 0.252
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.919
    Shell Resolution(Low) 2.998
    Number of Reflections(R-Free) 118
    Number of Reflections(R-Work) 2691
    R-Factor(R-Work) 0.243
    R-Factor(R-Free) 0.312
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.998
    Shell Resolution(Low) 3.086
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2614
    R-Factor(R-Work) 0.225
    R-Factor(R-Free) 0.273
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.086
    Shell Resolution(Low) 3.185
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2694
    R-Factor(R-Work) 0.201
    R-Factor(R-Free) 0.22
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.185
    Shell Resolution(Low) 3.299
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2594
    R-Factor(R-Work) 0.181
    R-Factor(R-Free) 0.203
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.299
    Shell Resolution(Low) 3.431
    Number of Reflections(R-Free) 155
    Number of Reflections(R-Work) 2637
    R-Factor(R-Work) 0.189
    R-Factor(R-Free) 0.235
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.431
    Shell Resolution(Low) 3.587
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2535
    R-Factor(R-Work) 0.191
    R-Factor(R-Free) 0.227
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.587
    Shell Resolution(Low) 3.776
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2584
    R-Factor(R-Work) 0.177
    R-Factor(R-Free) 0.23
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.776
    Shell Resolution(Low) 4.013
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2566
    R-Factor(R-Work) 0.141
    R-Factor(R-Free) 0.169
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.013
    Shell Resolution(Low) 4.323
    Number of Reflections(R-Free) 167
    Number of Reflections(R-Work) 2522
    R-Factor(R-Work) 0.125
    R-Factor(R-Free) 0.134
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.323
    Shell Resolution(Low) 4.757
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2551
    R-Factor(R-Work) 0.122
    R-Factor(R-Free) 0.167
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.757
    Shell Resolution(Low) 5.444
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2555
    R-Factor(R-Work) 0.15
    R-Factor(R-Free) 0.174
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 5.444
    Shell Resolution(Low) 6.855
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2525
    R-Factor(R-Work) 0.188
    R-Factor(R-Free) 0.219
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 6.855
    Shell Resolution(Low) 45.068
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2396
    R-Factor(R-Work) 0.164
    R-Factor(R-Free) 0.153
    Percent Reflections(Observed) 90.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 15.982
    f_plane_restr 0.006
    f_chiral_restr 0.09
    f_angle_d 1.251
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 6272
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 146
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XScale
    Structure Solution phenix.autosol
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    data extraction pdb_extract version: 3.100
    refinement phenix