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X-RAY DIFFRACTION
Materials and Methods page
4H3X
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 7
    Temperature 293.0
    Details protein: hMMP-9-WT 5.5 mg/mL 120 milli-M acetohydroxamic acid. Reservoir: 10% PEG 20,000, 60mM MES pH 5.5 + 18% MPEG 5,000, 0.08 M imidazole piperidine; pH 8.5, 0.05 M NaCl. Cryoprotectant: 10% Di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10K, 10% PCTP 50/50, 200mM NaCl , VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 40.11 α = 90
    b = 97.94 β = 111.73
    c = 46.08 γ = 90
     
    Space Group
    Space Group Name:    P 1 21 1
     
     
  •   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 2011-01-31
     
    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 0.8726
    Site ESRF
    Beamline ID23-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.76
    Resolution(Low) 50
    Number Reflections(All) 32612
    Number Reflections(Observed) 31957
    Percent Possible(Observed) 98.0
    R Merge I(Observed) 0.136
    B(Isotropic) From Wilson Plot 24.441
    Redundancy 4.23
     
    High Resolution Shell Details
    Resolution(High) 1.76
    Resolution(Low) 1.87
    Percent Possible(All) 94.2
    R Merge I(Observed) 0.666
    Mean I Over Sigma(Observed) 2.33
    R-Sym I(Observed) 0.582
    Redundancy 4.13
    Number Unique Reflections(All) 5246
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.764
    Resolution(Low) 42.806
    Cut-off Sigma(I) -3.0
    Cut-off Sigma(F) 2.0
    Number of Reflections(all) 31957
    Number of Reflections(Observed) 31949
    Number of Reflections(R-Free) 1598
    Percent Reflections(Observed) 98.28
    R-Factor(Observed) 0.1993
    R-Work 0.1964
    R-Free 0.2541
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7642
    Shell Resolution(Low) 1.8211
    Number of Reflections(Observed) 2598
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2598
    R-Factor(R-Work) 0.2696
    R-Factor(R-Free) 0.3117
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8211
    Shell Resolution(Low) 1.8862
    Number of Reflections(Observed) 2723
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2723
    R-Factor(R-Work) 0.2343
    R-Factor(R-Free) 0.3088
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8862
    Shell Resolution(Low) 1.9618
    Number of Reflections(Observed) 2754
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2754
    R-Factor(R-Work) 0.2077
    R-Factor(R-Free) 0.2585
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9618
    Shell Resolution(Low) 2.051
    Number of Reflections(Observed) 2748
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2748
    R-Factor(R-Work) 0.2
    R-Factor(R-Free) 0.2444
    Percent Reflections(Observed) 98.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.051
    Shell Resolution(Low) 2.1592
    Number of Reflections(Observed) 2769
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2769
    R-Factor(R-Work) 0.1875
    R-Factor(R-Free) 0.238
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1592
    Shell Resolution(Low) 2.2944
    Number of Reflections(Observed) 2788
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2788
    R-Factor(R-Work) 0.1984
    R-Factor(R-Free) 0.2603
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2944
    Shell Resolution(Low) 2.4716
    Number of Reflections(Observed) 2762
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2762
    R-Factor(R-Work) 0.1969
    R-Factor(R-Free) 0.3139
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4716
    Shell Resolution(Low) 2.7203
    Number of Reflections(Observed) 2789
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2789
    R-Factor(R-Work) 0.1991
    R-Factor(R-Free) 0.2359
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7203
    Shell Resolution(Low) 3.1138
    Number of Reflections(Observed) 2776
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2776
    R-Factor(R-Work) 0.1961
    R-Factor(R-Free) 0.2836
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1138
    Shell Resolution(Low) 3.9226
    Number of Reflections(Observed) 2807
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2807
    R-Factor(R-Work) 0.1764
    R-Factor(R-Free) 0.2212
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9226
    Shell Resolution(Low) 42.8181
    Number of Reflections(Observed) 2837
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2837
    R-Factor(R-Work) 0.1892
    R-Factor(R-Free) 0.2333
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.074
    f_dihedral_angle_d 18.451
    f_angle_d 1.03
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2608
    Nucleic Acid Atoms 0
    Heterogen Atoms 121
    Solvent Atoms 380
     
     
  •   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