POP-OUT | CLOSE

An Information Portal to 105212 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4GZI
  •   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, 0.2 mM laminarahexose, streak seeding, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 54.9 α = 90
    b = 49.27 β = 98.38
    c = 57.08 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 2006-07-02
     
    Diffraction Radiation
    Monochromator Ge(111) triangular bent crystal
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type EMBL/DESY, HAMBURG BEAMLINE X11
    Wavelength List 0.81620
    Site EMBL/DESY, HAMBURG
    Beamline X11
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.68
    Resolution(Low) 30
    Number Reflections(All) 34231
    Number Reflections(Observed) 34231
    Percent Possible(Observed) 99.0
    R Merge I(Observed) 0.069
    B(Isotropic) From Wilson Plot 24.6
    Redundancy 6.2
     
    High Resolution Shell Details
    Resolution(High) 1.68
    Resolution(Low) 1.74
    Percent Possible(All) 92.7
    R Merge I(Observed) 0.264
    Mean I Over Sigma(Observed) 5.1
    Redundancy 4.8
    Number Unique Reflections(All) 3131
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.68
    Resolution(Low) 20.0
    Cut-off Sigma(I) -3.0
    Number of Reflections(all) 33126
    Number of Reflections(Observed) 33126
    Number of Reflections(R-Free) 1076
    Percent Reflections(Observed) 99.04
    R-Factor(All) 0.1375
    R-Factor(Observed) 0.1375
    R-Work 0.1364
    R-Free 0.1713
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 17.54
    Anisotropic B[1][1] -0.06
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] -1.05
    Anisotropic B[2][2] -0.82
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.58
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.68
    Shell Resolution(Low) 1.723
    Number of Reflections(Observed) 2219
    Number of Reflections(R-Free) 66
    Number of Reflections(R-Work) 2219
    R-Factor(R-Work) 0.157
    R-Factor(R-Free) 0.204
    Percent Reflections(Observed) 91.55
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.885
    r_scbond_it 2.769
    r_mcangle_it 1.55
    r_mcbond_other 0.303
    r_mcbond_it 1.363
    r_nbd_refined 0.215
    r_gen_planes_other 0.001
    r_gen_planes_refined 0.008
    r_chiral_restr 0.11
    r_dihedral_angle_4_deg 15.453
    r_dihedral_angle_3_deg 11.751
    r_dihedral_angle_2_deg 32.25
    r_dihedral_angle_1_deg 6.233
    r_angle_other_deg 0.884
    r_angle_refined_deg 1.567
    r_bond_other_d 0.002
    r_bond_refined_d 0.017
    r_nbd_other 0.177
    r_nbtor_refined 0.184
    r_nbtor_other 0.102
    r_xyhbond_nbd_refined 0.128
    r_symmetry_vdw_refined 0.135
    r_symmetry_vdw_other 0.225
    r_symmetry_hbond_refined 0.116
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2509
    Nucleic Acid Atoms 0
    Heterogen Atoms 34
    Solvent Atoms 338
     
     
  •   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