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X-RAY DIFFRACTION
Materials and Methods page
4DZ7
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.8
    Temperature 298.0
    Details 1.6M Na-Citrate and 50 mM Tris-Cl at pH 7.8 used as precipitant solution. DMSO was used to dissolve the inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 42.29 α = 90
    b = 41.28 β = 104.13
    c = 72.06 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++
    Collection Date 2010-07-26
     
    Diffraction Radiation
    Monochromator Varimax Optics
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source ROTATING ANODE
    Type RIGAKU RUH3R
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 1.49
    Resolution(Low) 50
    Number Reflections(All) 39684
    Number Reflections(Observed) 38255
    Percent Possible(Observed) 96.4
    R Merge I(Observed) 0.07
    Redundancy 5.4
     
    High Resolution Shell Details
    Resolution(High) 1.49
    Resolution(Low) 1.54
    Percent Possible(All) 90.1
    R Merge I(Observed) 0.261
    Redundancy 5.1
    Number Unique Reflections(All) 3569
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.491
    Resolution(Low) 25.346
    Cut-off Sigma(F) 1.36
    Number of Reflections(Observed) 38255
    Number of Reflections(R-Free) 1895
    Percent Reflections(Observed) 96.68
    R-Factor(Observed) 0.1574
    R-Work 0.1564
    R-Free 0.1782
    R-Free Selection Details Random
     
    Temperature Factor Modeling
    Mean Isotropic B Value 16.899
    Anisotropic B[1][1] -1.0026
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0378
    Anisotropic B[2][2] -0.8785
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.8811
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.491
    Shell Resolution(Low) 1.5281
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2442
    R-Factor(R-Work) 0.3699
    R-Factor(R-Free) 0.3572
    Percent Reflections(Observed) 91.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5281
    Shell Resolution(Low) 1.5694
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2508
    R-Factor(R-Work) 0.2778
    R-Factor(R-Free) 0.2863
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5694
    Shell Resolution(Low) 1.6156
    Number of Reflections(R-Free) 124
    Number of Reflections(R-Work) 2488
    R-Factor(R-Work) 0.2174
    R-Factor(R-Free) 0.2794
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6156
    Shell Resolution(Low) 1.6678
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2538
    R-Factor(R-Work) 0.173
    R-Factor(R-Free) 0.1786
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6678
    Shell Resolution(Low) 1.7274
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2575
    R-Factor(R-Work) 0.1417
    R-Factor(R-Free) 0.1329
    Percent Reflections(Observed) 95.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7274
    Shell Resolution(Low) 1.7965
    Number of Reflections(R-Free) 127
    Number of Reflections(R-Work) 2570
    R-Factor(R-Work) 0.1311
    R-Factor(R-Free) 0.1674
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7965
    Shell Resolution(Low) 1.8782
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2583
    R-Factor(R-Work) 0.1271
    R-Factor(R-Free) 0.1831
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8782
    Shell Resolution(Low) 1.9772
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2617
    R-Factor(R-Work) 0.1334
    R-Factor(R-Free) 0.1427
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9772
    Shell Resolution(Low) 2.101
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2608
    R-Factor(R-Work) 0.1348
    R-Factor(R-Free) 0.1538
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.101
    Shell Resolution(Low) 2.2632
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2636
    R-Factor(R-Work) 0.1431
    R-Factor(R-Free) 0.1957
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2632
    Shell Resolution(Low) 2.4908
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2669
    R-Factor(R-Work) 0.1394
    R-Factor(R-Free) 0.1488
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4908
    Shell Resolution(Low) 2.8507
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2682
    R-Factor(R-Work) 0.1451
    R-Factor(R-Free) 0.1719
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8507
    Shell Resolution(Low) 3.59
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2701
    R-Factor(R-Work) 0.1487
    R-Factor(R-Free) 0.1718
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.59
    Shell Resolution(Low) 25.3498
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2778
    R-Factor(R-Work) 0.1691
    R-Factor(R-Free) 0.1839
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_dihedral_angle_d 12.945
    f_plane_restr 0.007
    f_chiral_restr 0.092
    f_angle_d 1.371
    f_bond_d 0.01
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2049
    Nucleic Acid Atoms 0
    Heterogen Atoms 28
    Solvent Atoms 208
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CrystalClear
    Data Reduction (intensity integration) HKL
    Data Reduction (data scaling) HKL
    Structure Solution phenix
    Structure Refinement PHENIX (phenix.refine: 1.7.2_869)
     
    Software
    data extraction pdb_extract version: 3.10
    refinement phenix
    data reduction HKL