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X-RAY DIFFRACTION
Materials and Methods page
4GR8
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 293.0
    Details protein: hMMP12 F171D 848 microM. reservoir: 24% PEG 10000, 0.2 M imidazole malate pH 8.5. CRYOPROTECTANT: 27% PEG 8000, 15% monomethyl-PEG 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 = 67.83 α = 90
    b = 61.47 β = 90
    c = 33.46 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 mirrors
    Collection Date 2010-04-24
     
    Diffraction Radiation
    Monochromator Si 111 CHANNEL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID14-4
    Wavelength List 0.9765
    Site ESRF
    Beamline ID14-4
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -4.0
    Resolution(High) 1.3
    Resolution(Low) 50
    Number Reflections(All) 35305
    Number Reflections(Observed) 35086
    Percent Possible(Observed) 99.4
    R Merge I(Observed) 0.098
    B(Isotropic) From Wilson Plot 17.669
    Redundancy 7.56
     
    High Resolution Shell Details
    Resolution(High) 1.3
    Resolution(Low) 1.38
    Percent Possible(All) 97.7
    R Merge I(Observed) 0.86
    Mean I Over Sigma(Observed) 2.47
    R-Sym I(Observed) 0.798
    Redundancy 7.16
    Number Unique Reflections(All) 5602
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.299
    Resolution(Low) 30.008
    Cut-off Sigma(I) -3.0
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 35086
    Number of Reflections(Observed) 35069
    Number of Reflections(R-Free) 1753
    Percent Reflections(Observed) 99.37
    R-Factor(Observed) 0.178
    R-Work 0.1767
    R-Free 0.2027
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.2988
    Shell Resolution(Low) 1.3339
    Number of Reflections(Observed) 2411
    Number of Reflections(R-Free) 125
    Number of Reflections(R-Work) 2411
    R-Factor(R-Work) 0.2661
    R-Factor(R-Free) 0.279
    Percent Reflections(Observed) 96.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3339
    Shell Resolution(Low) 1.3732
    Number of Reflections(Observed) 2546
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2546
    R-Factor(R-Work) 0.2353
    R-Factor(R-Free) 0.2661
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.3732
    Shell Resolution(Low) 1.4175
    Number of Reflections(Observed) 2526
    Number of Reflections(R-Free) 133
    Number of Reflections(R-Work) 2526
    R-Factor(R-Work) 0.2194
    R-Factor(R-Free) 0.2398
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4175
    Shell Resolution(Low) 1.4681
    Number of Reflections(Observed) 2540
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2540
    R-Factor(R-Work) 0.208
    R-Factor(R-Free) 0.2395
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4681
    Shell Resolution(Low) 1.5269
    Number of Reflections(Observed) 2553
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2553
    R-Factor(R-Work) 0.2057
    R-Factor(R-Free) 0.2421
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5269
    Shell Resolution(Low) 1.5964
    Number of Reflections(Observed) 2556
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2556
    R-Factor(R-Work) 0.185
    R-Factor(R-Free) 0.2034
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5964
    Shell Resolution(Low) 1.6806
    Number of Reflections(Observed) 2554
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2554
    R-Factor(R-Work) 0.1778
    R-Factor(R-Free) 0.2067
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6806
    Shell Resolution(Low) 1.7859
    Number of Reflections(Observed) 2547
    Number of Reflections(R-Free) 134
    Number of Reflections(R-Work) 2547
    R-Factor(R-Work) 0.1794
    R-Factor(R-Free) 0.183
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7859
    Shell Resolution(Low) 1.9237
    Number of Reflections(Observed) 2569
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2569
    R-Factor(R-Work) 0.1658
    R-Factor(R-Free) 0.1999
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9237
    Shell Resolution(Low) 2.1173
    Number of Reflections(Observed) 2598
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2598
    R-Factor(R-Work) 0.165
    R-Factor(R-Free) 0.197
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1173
    Shell Resolution(Low) 2.4235
    Number of Reflections(Observed) 2593
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2593
    R-Factor(R-Work) 0.1697
    R-Factor(R-Free) 0.1913
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4235
    Shell Resolution(Low) 3.0529
    Number of Reflections(Observed) 2635
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2635
    R-Factor(R-Work) 0.172
    R-Factor(R-Free) 0.2091
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0529
    Shell Resolution(Low) 30.0156
    Number of Reflections(Observed) 2688
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2688
    R-Factor(R-Work) 0.1577
    R-Factor(R-Free) 0.1789
    Percent Reflections(Observed) 97.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.077
    f_dihedral_angle_d 16.521
    f_angle_d 1.154
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1191
    Nucleic Acid Atoms 0
    Heterogen Atoms 47
    Solvent Atoms 197
     
     
  •   Software and Computing Hide
    Computing
    Data Collection CBASS
    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 CBASS