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X-RAY DIFFRACTION
Materials and Methods page
3TVC
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 5.5
    Temperature 293.0
    Details PROTEIN-INHIBITOR SOLUTION: MMP13 AT 20 MG/ML CO-CRYSTALLIZED WITH E3P AT 1.1 MILLI-M. RESERVOIR SOLUTION: 17.5% PEG 20K, 0.1 M MES, 0.02 M NACL. CRYOPROTECTANT: 5% DIETHYLENE GLYCOL, 5% ETHYLENE GLYCOL, 5% MPD, 5% PROPYLENE GLYCOL, 5% DMSO, 5% GLYCEROL, 0.005 M 3-(-PYRIDINIO)-1-PROPANESULFONATE, 10% PEG 20K, 0.033 M SODIUM ACETATE, 0.033 M ADA, 0.033 M BICINE, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 60.3 α = 90
    b = 85.16 β = 90
    c = 40.92 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   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 focusing
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID23-1
    Wavelength List 0.972420
    Site ESRF
    Beamline ID23-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2.43
    Resolution(Low) 85.1
    Number Reflections(All) 8412
    Number Reflections(Observed) 8151
    Percent Possible(Observed) 96.9
    R Merge I(Observed) 0.29
    B(Isotropic) From Wilson Plot 35.49
    Redundancy 7.21
     
    High Resolution Shell Details
    Resolution(High) 2.43
    Resolution(Low) 2.59
    Percent Possible(All) 87.4
    R Merge I(Observed) 1.399
    Mean I Over Sigma(Observed) 2.81
    R-Sym I(Observed) 1.29
    Redundancy 6.63
    Number Unique Reflections(All) 1231
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.43
    Resolution(Low) 40.916
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 1.34
    Number of Reflections(all) 8377
    Number of Reflections(Observed) 8127
    Number of Reflections(R-Free) 369
    Percent Reflections(Observed) 97.02
    R-Factor(Observed) 0.1654
    R-Work 0.1622
    R-Free 0.2341
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 24.782
    Anisotropic B[1][1] -2.7543
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] 1.2548
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 1.4995
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4304
    Shell Resolution(Low) 2.782
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2389
    R-Factor(R-Work) 0.2217
    R-Factor(R-Free) 0.327
    Percent Reflections(Observed) 93.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.782
    Shell Resolution(Low) 3.5047
    Number of Reflections(R-Free) 122
    Number of Reflections(R-Work) 2627
    R-Factor(R-Work) 0.1599
    R-Factor(R-Free) 0.2376
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.5047
    Shell Resolution(Low) 40.9215
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2742
    R-Factor(R-Work) 0.1433
    R-Factor(R-Free) 0.1965
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.083
    f_dihedral_angle_d 21.949
    f_angle_d 1.121
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1347
    Nucleic Acid Atoms 0
    Heterogen Atoms 58
    Solvent Atoms 105
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XSCALE
    Structure Solution PHASER_MR
    Structure Refinement PHENIX (phenix.refine)
     
    Software
    refinement PHENIX version: (phenix.refine)
    model building PHASER_MR
    data collection DNA