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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
2ID0
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7.5
    Temperature 298.0
    Details 25.5% PEG 2000 MME, 0.36 M MgCl2, 0.5 mM MnCl2, 5 mM DTT, 2 mM 3',5'-ADP, 0.1 M Tris-Cl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 55.76 α = 107.8
    b = 118.43 β = 98.36
    c = 122.38 γ = 91.4
     
    Space Group
    Space Group Name:    P 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315
    Collection Date 2005-11-18
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 8-BM
    Wavelength List 0.9790
    Site APS
    Beamline 8-BM
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.34
    Resolution(Low) 17.95
    Number Reflections(Observed) 117653
    Percent Possible(Observed) 92.7
    R Merge I(Observed) 0.074
    Redundancy 3.9
     
    High Resolution Shell Details
    Resolution(High) 2.34
    Resolution(Low) 2.42
    Percent Possible(All) 69.6
    R Merge I(Observed) 0.372
    Mean I Over Sigma(Observed) 2.8
    Redundancy 3.0
    Number Unique Reflections(All) 8815
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 2.35
    Resolution(Low) 17.95
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 100806
    Number of Reflections(R-Free) 5045
    Percent Reflections(Observed) 82.3
    R-Factor(Observed) 0.227
    R-Work 0.223
    R-Free 0.286
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 54.291
    Anisotropic B[1][1] -0.29
    Anisotropic B[1][2] -0.16
    Anisotropic B[1][3] -0.24
    Anisotropic B[2][2] -0.3
    Anisotropic B[2][3] -0.59
    Anisotropic B[3][3] 0.16
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.35
    Shell Resolution(Low) 2.41
    Number of Reflections(Observed) 4332
    Number of Reflections(R-Free) 181
    Number of Reflections(R-Work) 4151
    R-Factor(R-Work) 0.283
    R-Factor(R-Free) 0.335
    Percent Reflections(Observed) 48.7
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.683
    r_scbond_it 2.415
    r_mcangle_it 1.565
    r_mcbond_it 1.021
    r_symmetry_hbond_refined 0.181
    r_bond_refined_d 0.017
    r_angle_refined_deg 1.564
    r_dihedral_angle_1_deg 6.405
    r_dihedral_angle_2_deg 35.222
    r_dihedral_angle_3_deg 17.61
    r_dihedral_angle_4_deg 21.067
    r_chiral_restr 0.097
    r_gen_planes_refined 0.006
    r_nbd_refined 0.232
    r_nbtor_refined 0.311
    r_xyhbond_nbd_refined 0.173
    r_symmetry_vdw_refined 0.216
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 19529
    Nucleic Acid Atoms 0
    Heterogen Atoms 4
    Solvent Atoms 287
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC QUANTUM
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution SHAKE-N-BAKE
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 2.000
    refinement REFMAC5 version: 5.2.0019