POP-OUT | CLOSE

An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4AYR
  •   Crystallization Hide
    Crystallization Experiments
    pH 6.5
    Details 0.2 M AMMONIUM ACTETATE, 0.1 M BIS-TRIS PH 6.5, 22% WT/VOL PEG 3350
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 143.92 α = 90
    b = 143.92 β = 90
    c = 50.19 γ = 120
     
    Space Group
    Space Group Name:    H 3
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL (PILATUS 2M)
    Type DECTRIS
    Details MIRRORS
    Collection Date 2012-03-08
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type DIAMOND BEAMLINE I04-1
    Wavelength 0.9173
    Site DIAMOND
    Beamline I04-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) 2.0
    Resolution(High) 1.1
    Resolution(Low) 46.55
    Number Reflections(Observed) 140945
    Percent Possible(Observed) 89.6
    R Merge I(Observed) 0.04
    Redundancy 9.1
     
    High Resolution Shell Details
    Resolution(High) 1.1
    Resolution(Low) 1.16
    Percent Possible(All) 49.5
    R Merge I(Observed) 0.21
    Mean I Over Sigma(Observed) 6.7
    Redundancy 4.2
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.1
    Resolution(Low) 46.6
    Number of Reflections(Observed) 133840
    Number of Reflections(R-Free) 7105
    Percent Reflections(Observed) 89.53
    R-Factor(Observed) 0.08362
    R-Work 0.08264
    R-Free 0.10208
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 9.843
    Anisotropic B[1][1] -0.05
    Anisotropic B[1][2] -0.03
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.05
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.08
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.1
    Shell Resolution(Low) 1.129
    Number of Reflections(R-Free) 241
    Number of Reflections(R-Work) 4702
    R-Factor(R-Work) 0.117
    R-Factor(R-Free) 0.129
    Percent Reflections(Observed) 42.45
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_sphericity_bonded 7.229
    r_sphericity_free 36.735
    r_rigid_bond_restr 1.588
    r_nbd_refined 0.275
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.008
    r_chiral_restr 0.28
    r_dihedral_angle_4_deg 16.668
    r_dihedral_angle_3_deg 12.157
    r_dihedral_angle_2_deg 33.099
    r_dihedral_angle_1_deg 6.001
    r_angle_other_deg 0.816
    r_angle_refined_deg 1.394
    r_bond_other_d 0.001
    r_bond_refined_d 0.01
    r_nbd_other 0.172
    r_nbtor_refined 0.188
    r_nbtor_other 0.085
    r_xyhbond_nbd_refined 0.171
    r_xyhbond_nbd_other 0.019
    r_metal_ion_refined 0.054
    r_symmetry_vdw_refined 0.338
    r_symmetry_vdw_other 0.274
    r_symmetry_hbond_refined 0.338
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 3429
    Nucleic Acid Atoms 0
    Heterogen Atoms 84
    Solvent Atoms 724
     
     
  •   Software and Computing Hide
    Computing
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) SCALA
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.7.0025
     
    Software
    refinement REFMAC version: 5.7.0025
    model building MOLREP