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An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
1UGU
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 6.5
    Temperature 293.0
    Details PEGMME 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 40.35 α = 90
    b = 40.35 β = 90
    c = 118 γ = 120
     
    Space Group
    Space Group Name:    P 65
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARRESEARCH
    Collection Date 2003-02-07
     
    Diffraction Radiation
    Monochromator Si(111) double monochromator
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SPRING-8 BEAMLINE BL41XU
    Wavelength List 0.650
    Site SPRING-8
    Beamline BL41XU
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 1.2
    Resolution(Low) 35
    Number Reflections(All) 33512
    Number Reflections(Observed) 31902
    Percent Possible(Observed) 94.5
    B(Isotropic) From Wilson Plot 14.3
    Redundancy 8.3
     
    High Resolution Shell Details
    Resolution(High) 1.2
    Resolution(Low) 1.24
    Percent Possible(All) 82.4
    Mean I Over Sigma(Observed) 3.4
    R-Sym I(Observed) 0.368
    Redundancy 5.6
    Number Unique Reflections(All) 3170
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.2
    Resolution(Low) 34.92
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 31742
    Number of Reflections(Observed) 31742
    Number of Reflections(R-Free) 1699
    R-Factor(All) 0.16658
    R-Factor(Observed) 0.16658
    R-Work 0.16523
    R-Free 0.19113
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 14.293
    Anisotropic B[1][1] 0.49
    Anisotropic B[1][2] 0.25
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 0.49
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.74
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.202
    Shell Resolution(Low) 1.233
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2150
    R-Factor(R-Work) 0.261
    R-Factor(R-Free) 0.272
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 2.835
    r_nbtor_other 0.1
    r_nbd_other 0.291
    r_nbd_refined 0.287
    r_gen_planes_other 0.008
    r_gen_planes_refined 0.008
    r_chiral_restr 0.098
    r_dihedral_angle_1_deg 5.941
    r_angle_other_deg 0.806
    r_angle_refined_deg 1.44
    r_bond_other_d 0.0
    r_bond_refined_d 0.011
    r_xyhbond_nbd_refined 0.243
    r_symmetry_vdw_refined 0.156
    r_symmetry_vdw_other 0.212
    r_symmetry_hbond_refined 0.25
    r_mcbond_it 1.187
    r_mcangle_it 1.853
    r_scbond_it 2.141
    r_scangle_it 3.243
    r_rigid_bond_restr 1.15
    r_sphericity_free 2.973
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 949
    Nucleic Acid Atoms 0
    Heterogen Atoms 11
    Solvent Atoms 180
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) SCALEPACK
    Structure Solution CNS
    Structure Refinement REFMAC 5.1.24
     
    Software
    refinement REFMAC version: 5.1.24