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An Information Portal to 110790 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3UR8
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4.6
    Temperature 292.0
    Details 0.1 M sodium acetate, 0.2 M ammonium acetate, 25% PEG 4000, 15 mM glucose, streak seeding, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 75.36 α = 90
    b = 49.06 β = 103.56
    c = 82.62 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector FLAT PANEL
    Type MAR555 FLAT PANEL
    Details mirrors
    Collection Date 2007-02-04
     
    Diffraction Radiation
    Monochromator Ge(111) triangular bent crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type EMBL/DESY, HAMBURG BEAMLINE X11
    Wavelength List 0.8148
    Site EMBL/DESY, HAMBURG
    Beamline X11
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.26
    Resolution(Low) 40
    Number Reflections(All) 151662
    Number Reflections(Observed) 151662
    Percent Possible(Observed) 95.4
    R Merge I(Observed) 0.059
    B(Isotropic) From Wilson Plot 12.9
    Redundancy 4.6
     
    High Resolution Shell Details
    Resolution(High) 1.26
    Resolution(Low) 1.31
    Percent Possible(All) 93.8
    R Merge I(Observed) 0.467
    Mean I Over Sigma(Observed) 2.0
    Redundancy 3.3
    Number Unique Reflections(All) 14787
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.26
    Resolution(Low) 19.54
    Number of Reflections(all) 149903
    Number of Reflections(Observed) 149903
    Number of Reflections(R-Free) 1654
    Percent Reflections(Observed) 95.04
    R-Factor(All) 0.14277
    R-Factor(Observed) 0.14277
    R-Work 0.14235
    R-Free 0.18244
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Anisotropic model of ADP parameters
    Mean Isotropic B Value 9.348
    Anisotropic B[1][1] 0.01
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.01
    Anisotropic B[2][2] -0.02
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.0
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.26
    Shell Resolution(Low) 1.29
    Number of Reflections(Observed) 10372
    Number of Reflections(R-Free) 119
    Number of Reflections(R-Work) 10372
    R-Factor(R-Work) 0.221
    R-Factor(R-Free) 0.278
    Percent Reflections(Observed) 89.75
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 5.096
    r_sphericity_free 10.821
    r_rigid_bond_restr 1.807
    r_scangle_it 4.627
    r_scbond_it 3.554
    r_mcangle_it 2.493
    r_mcbond_other 0.933
    r_mcbond_it 2.097
    r_nbd_refined 0.22
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.01
    r_chiral_restr 0.119
    r_dihedral_angle_4_deg 15.339
    r_dihedral_angle_3_deg 11.999
    r_dihedral_angle_2_deg 33.975
    r_dihedral_angle_1_deg 6.297
    r_angle_other_deg 1.044
    r_angle_refined_deg 1.744
    r_bond_other_d 0.001
    r_bond_refined_d 0.018
    r_nbd_other 0.173
    r_nbtor_refined 0.191
    r_nbtor_other 0.088
    r_xyhbond_nbd_refined 0.111
    r_symmetry_vdw_refined 0.156
    r_symmetry_vdw_other 0.264
    r_symmetry_hbond_refined 0.111
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5091
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 763
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MAR345dtb
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.2.0003
     
    Software
    refinement REFMAC version: 5.2.0003
    model building MOLREP
    data collection MAR345dtb