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An Information Portal to 108263 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3TT4
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 5.5
    Temperature 293.0
    Details MMP-8 at 400 micro-M co-crystallization with peptidic inhibitor with reservoir solution 17.5% PEG 20K, 0.1 M MES, 0.125 M NACL. VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K. Inhibitor exchange: 24hr soak in 25% PEG 4K instead of 17.5% PEG20K with 100 micro-M E1S inhibitor in 6 micro-L volume cryoprotectant is 12% PEG10K, 13.75% MPEG2K, 5% di-ethylene glycol, 10% 1,2-propanediol, 10% glycerol, 0.025 M MES PH 5.5, 30 sec cryoprotectant soak
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 32.72 α = 90
    b = 69.37 β = 90
    c = 70.31 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 CCD
    Type ADSC QUANTUM 315r
    Details bent cylindrical mirror
    Collection Date 2011-06-13
     
    Diffraction Radiation
    Monochromator horizontally diffracting Si (111) monochromator and Pt coated mirrors in Kirkpatrick-Baez geometry for focussing
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID23-1
    Wavelength List 0.97242
    Site ESRF
    Beamline ID23-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.88
    Resolution(Low) 60
    Number Reflections(All) 13650
    Number Reflections(Observed) 13397
    Percent Possible(Observed) 98.1
    R Merge I(Observed) 0.247
    B(Isotropic) From Wilson Plot 24.39
    Redundancy 5.26
     
    High Resolution Shell Details
    Resolution(High) 1.88
    Resolution(Low) 2.01
    Percent Possible(All) 99.6
    R Merge I(Observed) 1.026
    Mean I Over Sigma(Observed) 2.08
    R-Sym I(Observed) 0.919
    Redundancy 5.2
    Number Unique Reflections(All) 12439
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.88
    Resolution(Low) 34.69
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 12970
    Number of Reflections(Observed) 12729
    Number of Reflections(R-Free) 667
    Percent Reflections(Observed) 98.14
    R-Factor(Observed) 0.19409
    R-Work 0.19087
    R-Free 0.2578
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 21.835
    Anisotropic B[1][1] -1.73
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -1.79
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 3.53
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.88
    Shell Resolution(Low) 1.929
    Number of Reflections(R-Free) 58
    Number of Reflections(R-Work) 945
    R-Factor(R-Work) 0.325
    R-Factor(R-Free) 0.424
    Percent Reflections(Observed) 99.6
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.249
    r_scbond_it 3.103
    r_mcangle_it 2.071
    r_mcbond_it 1.278
    r_gen_planes_refined 0.011
    r_chiral_restr 0.24
    r_dihedral_angle_4_deg 21.05
    r_dihedral_angle_3_deg 16.025
    r_dihedral_angle_2_deg 33.691
    r_dihedral_angle_1_deg 7.547
    r_angle_refined_deg 2.012
    r_bond_refined_d 0.022
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1253
    Nucleic Acid Atoms 0
    Heterogen Atoms 42
    Solvent Atoms 171
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.5.0109
     
    Software
    refinement REFMAC version: 5.5.0109
    model building MOLREP
    data collection DNA