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X-RAY DIFFRACTION
Materials and Methods page
4GR3
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8
    Temperature 293.0
    Details Protein: hMMP12(F171D) 643 microM. Reservoir: 18% PEG 10000, 0.2 M imidazole malate pH 8.0. Cryoprotectant: 27% PEG 8000, 15% monomethylPEG 550, 10% glycerol, 0.09 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 68.96 α = 90
    b = 63.13 β = 90
    c = 37.31 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 4
    Details Toroidal mirror
    Collection Date 2009-09-20
     
    Diffraction Radiation
    Monochromator Si 111 CHANNEL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-2
    Wavelength List 0.9334
    Site ESRF
    Beamline ID14-2
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -4.0
    Resolution(High) 1.49
    Resolution(Low) 50
    Number Reflections(All) 27105
    Number Reflections(Observed) 27049
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.106
    B(Isotropic) From Wilson Plot 21.514
    Redundancy 7.9
     
    High Resolution Shell Details
    Resolution(High) 1.49
    Resolution(Low) 1.58
    Percent Possible(All) 98.9
    R Merge I(Observed) 1.17
    Mean I Over Sigma(Observed) 1.97
    R-Sym I(Observed) 1.1
    Redundancy 6.98
    Number Unique Reflections(All) 4273
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.494
    Resolution(Low) 46.565
    Cut-off Sigma(I) -3.0
    Cut-off Sigma(F) 2.0
    Number of Reflections(all) 27049
    Number of Reflections(Observed) 27033
    Number of Reflections(R-Free) 1352
    Percent Reflections(Observed) 99.76
    R-Factor(Observed) 0.1821
    R-Work 0.1803
    R-Free 0.2158
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4942
    Shell Resolution(Low) 1.5476
    Number of Reflections(Observed) 2482
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2482
    R-Factor(R-Work) 0.2757
    R-Factor(R-Free) 0.3122
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5476
    Shell Resolution(Low) 1.6096
    Number of Reflections(Observed) 2511
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2511
    R-Factor(R-Work) 0.2477
    R-Factor(R-Free) 0.2894
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6096
    Shell Resolution(Low) 1.6828
    Number of Reflections(Observed) 2549
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2549
    R-Factor(R-Work) 0.2265
    R-Factor(R-Free) 0.2741
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6828
    Shell Resolution(Low) 1.7715
    Number of Reflections(Observed) 2540
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2540
    R-Factor(R-Work) 0.214
    R-Factor(R-Free) 0.2571
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7715
    Shell Resolution(Low) 1.8825
    Number of Reflections(Observed) 2546
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2546
    R-Factor(R-Work) 0.1931
    R-Factor(R-Free) 0.2598
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8825
    Shell Resolution(Low) 2.0279
    Number of Reflections(Observed) 2567
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2567
    R-Factor(R-Work) 0.1814
    R-Factor(R-Free) 0.2178
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0279
    Shell Resolution(Low) 2.232
    Number of Reflections(Observed) 2560
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2560
    R-Factor(R-Work) 0.174
    R-Factor(R-Free) 0.2163
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.232
    Shell Resolution(Low) 2.5549
    Number of Reflections(Observed) 2567
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2567
    R-Factor(R-Work) 0.1702
    R-Factor(R-Free) 0.2171
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5549
    Shell Resolution(Low) 3.2188
    Number of Reflections(Observed) 2611
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2611
    R-Factor(R-Work) 0.1633
    R-Factor(R-Free) 0.187
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2188
    Shell Resolution(Low) 46.5872
    Number of Reflections(Observed) 2748
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2748
    R-Factor(R-Work) 0.159
    R-Factor(R-Free) 0.1828
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.073
    f_dihedral_angle_d 16.814
    f_angle_d 1.091
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1246
    Nucleic Acid Atoms 0
    Heterogen Atoms 50
    Solvent Atoms 295
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution MOLREP
    Structure Refinement PHENIX (phenix.refine: 1.8_1069)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.8_1069)
    model building MOLREP
    data collection DNA