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An Information Portal to 105097 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
4GD3
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION
    pH 5.9
    Temperature 298.0
    Details 12% PEG4000, 0.1M NaCl, 0.1M NaAc, 0.2M NH4Ac, 0.001M DTT, 0.02% DDM, Tris/HCl, 0.0003M NQNO (a menaquinone analog), pH 5.9, VAPOR DIFFUSION, temperature 298K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 126 α = 90
    b = 165.3 β = 90
    c = 212.8 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type PSI PILATUS 6M
    Collection Date 2012-06-29
     
    Diffraction Radiation
    Monochromator Si 111
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID29
    Wavelength List 0.97908
    Site ESRF
    Beamline ID29
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 3.2
    Resolution(Low) 49.12
    Number Reflections(All) 73321
    Number Reflections(Observed) 138472
    Percent Possible(Observed) 97.8
    R Merge I(Observed) 0.08
    B(Isotropic) From Wilson Plot 89.561
     
    High Resolution Shell Details
    Resolution(High) 3.2
    Resolution(Low) 3.3
    Percent Possible(All) 97.1
    R Merge I(Observed) 1.054
    Mean I Over Sigma(Observed) 1.16
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 3.3
    Resolution(Low) 25.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 67491
    Number of Reflections(Observed) 66832
    Number of Reflections(R-Free) 3298
    Percent Reflections(Observed) 99.27
    R-Factor(All) 0.2018
    R-Factor(Observed) 0.2018
    R-Work 0.1999
    R-Free 0.236
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model TLS + isotropic (possible thanks to tight ncs restraints)
    Mean Isotropic B Value 105.957
    Anisotropic B[1][1] 7.45
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -6.89
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.57
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.3
    Shell Resolution(Low) 3.384
    Number of Reflections(Observed) 4592
    Number of Reflections(R-Free) 229
    Number of Reflections(R-Work) 4592
    R-Factor(R-Work) 0.344
    R-Factor(R-Free) 0.348
    Percent Reflections(Observed) 99.24
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 3.834
    r_scbond_it 2.306
    r_mcangle_it 1.661
    r_mcbond_it 0.837
    r_gen_planes_refined 0.005
    r_chiral_restr 0.082
    r_dihedral_angle_4_deg 15.385
    r_dihedral_angle_3_deg 17.099
    r_dihedral_angle_2_deg 35.949
    r_dihedral_angle_1_deg 5.28
    r_angle_refined_deg 1.161
    r_bond_refined_d 0.011
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 30002
    Nucleic Acid Atoms 0
    Heterogen Atoms 316
    Solvent Atoms 40
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MXCuBE
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER
    Structure Refinement REFMAC 5.5.0109
     
    Software
    data extraction pdb_extract version: 3.11
    refinement REFMAC5
    molecular replacement Phaser
    data reduction Xscale