POP-OUT | CLOSE

An Information Portal to 106082 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4L8H
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 4.5
    Temperature 293.0
    Details 0.1 M sodium acetate, 0.2 M zinc acetate, 9% PEG 3000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 75.84 α = 90
    b = 75.84 β = 90
    c = 303.49 γ = 120
     
    Space Group
    Space Group Name:    P 65 2 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Details multilayer mirrors
    Collection Date 2013-02-01
     
    Diffraction Radiation
    Monochromator Double crystal monochromator, Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source synchrotron
    Type MAX II BEAMLINE I911-3
    Wavelength List 1.0000
    Site MAX II
    Beamline I911-3
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.4
    Resolution(Low) 40.06
    Number Reflections(All) 21342
    Number Reflections(Observed) 21342
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.09
    B(Isotropic) From Wilson Plot 34.937
    Redundancy 3.4
     
    High Resolution Shell Details
    Resolution(High) 2.4
    Resolution(Low) 2.53
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.614
    Mean I Over Sigma(Observed) 2.2
    Redundancy 3.5
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.4
    Resolution(Low) 37.63
    Number of Reflections(all) 21269
    Number of Reflections(Observed) 21269
    Number of Reflections(R-Free) 1089
    Percent Reflections(Observed) 99.85
    R-Factor(All) 0.25453
    R-Factor(Observed) 0.25453
    R-Work 0.25267
    R-Free 0.28839
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 34.194
    Anisotropic B[1][1] -0.02
    Anisotropic B[1][2] -0.01
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.02
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.03
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4
    Shell Resolution(Low) 2.462
    Number of Reflections(R-Free) 79
    Number of Reflections(R-Work) 1448
    R-Factor(R-Work) 0.368
    R-Factor(R-Free) 0.363
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.851
    r_scbond_it 2.404
    r_mcangle_it 1.908
    r_mcbond_it 1.02
    r_gen_planes_refined 0.007
    r_chiral_restr 0.094
    r_dihedral_angle_4_deg 15.915
    r_dihedral_angle_3_deg 14.496
    r_dihedral_angle_2_deg 35.344
    r_dihedral_angle_1_deg 6.843
    r_angle_refined_deg 1.67
    r_bond_refined_d 0.016
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1855
    Nucleic Acid Atoms 423
    Heterogen Atoms 6
    Solvent Atoms 90
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MARCCD
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.5.0110
     
    Software
    refinement REFMAC version: 5.5.0110
    model building MOLREP
    data collection MARCCD