POP-OUT | CLOSE

An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4JK9
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion
    pH 7.5
    Temperature 298.0
    Details 15% PEG 4000, 300mM MgCl2, 100mM Tris, pH 7.5, vapor diffusion, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 76.23 α = 90
    b = 78.29 β = 90
    c = 94.09 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 300 mm CCD
    Collection Date 2010-07-02
     
    Diffraction Radiation
    Monochromator Si
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source Synchrotron
    Type CLSI BEAMLINE 08ID-1
    Wavelength List 0.97949
    Site CLSI
    Beamline 08ID-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 1.0
    Observed Criterion Sigma(I) 1.0
    Resolution(High) 1.5
    Resolution(Low) 50
    Number Reflections(Observed) 80130
    Percent Possible(Observed) 88.1
    R Merge I(Observed) 0.067
    Redundancy 3.6
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.55
    Percent Possible(All) 96.3
    R Merge I(Observed) 0.447
    Redundancy 2.8
    Number Unique Reflections(All) 8619
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.5
    Resolution(Low) 34.27
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 80075
    Number of Reflections(R-Free) 4216
    Percent Reflections(Observed) 88.01
    R-Factor(Observed) 0.1661
    R-Work 0.1639
    R-Free 0.2049
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 22.4173
    Anisotropic B[1][1] -0.59
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.41
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.18
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5
    Shell Resolution(Low) 1.537
    Number of Reflections(R-Free) 335
    Number of Reflections(R-Work) 5890
    R-Factor(R-Work) 0.159
    R-Factor(R-Free) 0.251
    Percent Reflections(Observed) 93.51
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 4.693
    r_sphericity_free 11.068
    r_rigid_bond_restr 2.045
    r_scangle_it 5.308
    r_nbd_refined 0.235
    r_gen_planes_other 0.002
    r_gen_planes_refined 0.009
    r_chiral_restr 0.118
    r_dihedral_angle_4_deg 16.987
    r_dihedral_angle_3_deg 13.447
    r_dihedral_angle_2_deg 40.098
    r_dihedral_angle_1_deg 5.866
    r_angle_other_deg 0.885
    r_angle_refined_deg 1.814
    r_bond_other_d 0.001
    r_bond_refined_d 0.022
    r_nbd_other 0.186
    r_nbtor_refined 0.182
    r_nbtor_other 0.086
    r_xyhbond_nbd_refined 0.214
    r_metal_ion_refined 0.091
    r_symmetry_vdw_refined 0.209
    r_symmetry_vdw_other 0.248
    r_symmetry_hbond_refined 0.16
    r_mcbond_it 2.466
    r_mcbond_other 0.93
    r_mcangle_it 2.915
    r_scbond_it 4.084
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3575
    Nucleic Acid Atoms 0
    Heterogen Atoms 15
    Solvent Atoms 518
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CLS
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution REFMAC 5.2.0005
    Structure Refinement REFMAC 5.2.0005
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5 version: 5.2.0005
    data reduction SCALEPACK