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An Information Portal to 105339 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4GZJ
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 5.6
    Temperature 292.0
    Details 0.1 M sodium citrate, 0.2 M ammonium acetate, 24% PEG 8000, 0.4 mM laminarahexose, streak seeding, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 55.31 α = 90
    b = 49.2 β = 98.84
    c = 57.43 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 0.81480
    Site EMBL/DESY, HAMBURG
    Beamline X11
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.55
    Resolution(Low) 40
    Number Reflections(All) 44391
    Number Reflections(Observed) 44391
    Percent Possible(Observed) 100.0
    R Merge I(Observed) 0.091
    B(Isotropic) From Wilson Plot 21.2
    Redundancy 3.8
     
    High Resolution Shell Details
    Resolution(High) 1.55
    Resolution(Low) 1.61
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.68
    Mean I Over Sigma(Observed) 2.1
    Redundancy 3.8
    Number Unique Reflections(All) 4390
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.55
    Resolution(Low) 20.0
    Cut-off Sigma(I) -3.0
    Number of Reflections(all) 43213
    Number of Reflections(Observed) 43213
    Number of Reflections(R-Free) 1139
    Percent Reflections(Observed) 99.91
    R-Factor(All) 0.1515
    R-Factor(Observed) 0.1515
    R-Work 0.1507
    R-Free 0.1806
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 15.27
    Anisotropic B[1][1] -0.01
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -0.47
    Anisotropic B[2][2] -0.49
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.35
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.55
    Shell Resolution(Low) 1.59
    Number of Reflections(Observed) 3125
    Number of Reflections(R-Free) 95
    Number of Reflections(R-Work) 3125
    R-Factor(R-Work) 0.199
    R-Factor(R-Free) 0.286
    Percent Reflections(Observed) 99.26
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.674
    r_scbond_it 2.47
    r_mcangle_it 1.592
    r_mcbond_other 0.32
    r_mcbond_it 1.051
    r_nbd_refined 0.218
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.009
    r_chiral_restr 0.11
    r_dihedral_angle_4_deg 15.502
    r_dihedral_angle_3_deg 11.925
    r_dihedral_angle_2_deg 32.661
    r_dihedral_angle_1_deg 6.2
    r_angle_other_deg 0.887
    r_angle_refined_deg 1.644
    r_bond_other_d 0.001
    r_bond_refined_d 0.017
    r_nbd_other 0.173
    r_nbtor_refined 0.19
    r_nbtor_other 0.088
    r_xyhbond_nbd_refined 0.121
    r_symmetry_vdw_refined 0.134
    r_symmetry_vdw_other 0.195
    r_symmetry_hbond_refined 0.125
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2509
    Nucleic Acid Atoms 0
    Heterogen Atoms 57
    Solvent Atoms 356
     
     
  •   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