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X-RAY DIFFRACTION
Materials and Methods page
2AGI
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6
    Temperature 298.0
    Details ammonium sulfate, bis-tris propane, calcium chloride, benzamidine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 61.89 α = 90
    b = 63.56 β = 90
    c = 69.1 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 ADSC QUANTUM 4
    Collection Date 2003-10-17
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ALS BEAMLINE 8.3.1
    Wavelength List 1.00000
    Site ALS
    Beamline 8.3.1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.14
    Resolution(Low) 46.63
    Number Reflections(All) 88464
    Number Reflections(Observed) 88464
    Percent Possible(Observed) 99.64
    R Merge I(Observed) 0.04
    Redundancy 3.2
     
    High Resolution Shell Details
    Resolution(High) 1.14
    Resolution(Low) 1.2
    R Merge I(Observed) 0.284
    Mean I Over Sigma(Observed) 1.5
    R-Sym I(Observed) 0.284
    Redundancy 1.3
    Number Unique Reflections(All) 6920
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.14
    Resolution(Low) 46.63
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 88464
    Number of Reflections(Observed) 88464
    Number of Reflections(R-Free) 4449
    Percent Reflections(Observed) 99.64
    R-Factor(All) 0.117
    R-Factor(Observed) 0.117
    R-Work 0.116
    R-Free 0.138
    R-Free Selection Details inherited from PDB entry 2AGE
     
    Temperature Factor Modeling
    Isotropic Thermal Model anisotropic
    Mean Isotropic B Value 12.663
    Anisotropic B[1][1] -0.06
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.09
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.15
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.14
    Shell Resolution(Low) 1.17
    Number of Reflections(R-Free) 152
    Number of Reflections(R-Work) 2669
    R-Factor(R-Work) 0.356
    R-Factor(R-Free) 0.386
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 6.875
    r_sphericity_free 16.976
    r_rigid_bond_restr 3.471
    r_nbd_refined 0.377
    r_gen_planes_other 0.005
    r_gen_planes_refined 0.01
    r_chiral_restr 0.137
    r_dihedral_angle_4_deg 11.996
    r_dihedral_angle_3_deg 10.309
    r_dihedral_angle_2_deg 41.098
    r_dihedral_angle_1_deg 6.677
    r_angle_other_deg 1.904
    r_angle_refined_deg 1.869
    r_bond_other_d 0.007
    r_bond_refined_d 0.017
    r_nbd_other 0.27
    r_nbtor_other 0.102
    r_xyhbond_nbd_refined 0.181
    r_metal_ion_refined 0.121
    r_symmetry_vdw_refined 0.193
    r_symmetry_vdw_other 0.356
    r_symmetry_hbond_refined 0.229
    r_mcbond_it 3.083
    r_mcbond_other 2.198
    r_mcangle_it 3.977
    r_scbond_it 5.283
    r_scangle_it 6.73
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1654
    Nucleic Acid Atoms 0
    Heterogen Atoms 11
    Solvent Atoms 371
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) CCP4 (SCALA, TRUNCATE)
    Structure Solution EPMR
    Structure Refinement REFMAC 5.2
     
    Software
    refinement REFMAC version: 5.2
    model building EPMR
    data reduction TRUNCATE
    data reduction SCALA
    data collection MOSFLM