POP-OUT | CLOSE
 
X-RAY DIFFRACTION
Materials and Methods page
3BDC
  •   Crystallization Hide
    Crystallization Experiments
    Method vapor diffusion, hanging drop
    pH 8
    Temperature 277.0
    Details 17% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 8.0, vapor diffusion, hanging drop, temperature 277K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 31.1 α = 90
    b = 60.65 β = 94.44
    c = 36.95 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 110
     
    Diffraction Detector
    Detector CCD
    Type BRUKER APEX II
    Details multi-layer optics
    Collection Date 2007-09-05
     
    Diffraction Radiation
    Monochromator GE111
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SEALED TUBE
    Type OTHER
    Wavelength List 1.5418
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.8
    Resolution(Low) 31.5
    Number Reflections(Observed) 14206
    Percent Possible(Observed) 99.37
    Redundancy 13.18
     
    High Resolution Shell Details
    Resolution(High) 1.8
    Resolution(Low) 1.9
    Percent Possible(All) 100.0
    Mean I Over Sigma(Observed) 6.22
    R-Sym I(Observed) 0.415
    Redundancy 7.86
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.8
    Resolution(Low) 31.01
    Number of Reflections(all) 12767
    Number of Reflections(Observed) 10735
    Number of Reflections(R-Free) 1179
    Percent Reflections(Observed) 93.32
    R-Factor(Observed) 0.19556
    R-Work 0.1895
    R-Free 0.2512
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model isotropic
    Mean Isotropic B Value 22.944
    Anisotropic B[1][1] 0.0
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.01
    Anisotropic B[2][2] 0.0
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.01
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8
    Shell Resolution(Low) 1.847
    Number of Reflections(R-Free) 83
    Number of Reflections(R-Work) 737
    R-Factor(R-Work) 0.273
    R-Factor(R-Free) 0.362
    Percent Reflections(Observed) 85.15
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.785
    r_scbond_it 2.535
    r_mcangle_it 1.629
    r_mcbond_it 1.11
    r_nbd_refined 0.23
    r_gen_planes_refined 0.006
    r_chiral_restr 0.121
    r_dihedral_angle_4_deg 9.345
    r_dihedral_angle_3_deg 16.675
    r_dihedral_angle_2_deg 34.112
    r_dihedral_angle_1_deg 5.907
    r_angle_refined_deg 1.772
    r_bond_refined_d 0.017
    r_nbtor_refined 0.31
    r_xyhbond_nbd_refined 0.139
    r_symmetry_vdw_refined 0.121
    r_symmetry_hbond_refined 0.135
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1033
    Nucleic Acid Atoms 0
    Heterogen Atoms 26
    Solvent Atoms 106
     
     
  •   Software and Computing Hide
    Computing
    Data Collection APEX
    Data Reduction (intensity integration) SAINT
    Data Reduction (data scaling) SAINT
    Structure Solution PHASER
    Structure Refinement REFMAC 5.2.0019
     
    Software
    data extraction pdb_extract version: 3.000
    refinement REFMAC5 version: 5.2.0019
    molecular replacement Phaser
    data processing SAINT version: V7.34A
    collection/data indexing SAINT