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X-RAY DIFFRACTION
Materials and Methods page
4H49
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6
    Temperature 293.0
    Details Protein: hMMP12 F171D 0.78 milli-M + 0.010 M AHA. Reservoir: 17% PEG 20.000, 0.2 M imidazole malate, pH 6.0, 0.25 M NaCl. Cryoprotectant: 10% di-ethylene glycol + 10% glycerol + 10% 1,2-propanediol, 25% M PEG 5.000, 0.1 M BES pH 5.5., VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 47.44 α = 90
    b = 106.49 β = 94.96
    c = 65.88 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 PIXEL
    Type DECTRIS PILATUS 6M
    Details mirrors
    Collection Date 2012-07-04
     
    Diffraction Radiation
    Monochromator Si 111 CHANNEL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SOLEIL BEAMLINE PROXIMA 1
    Wavelength List 0.98011
    Site SOLEIL
    Beamline PROXIMA 1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 2.16
    Resolution(Low) 50
    Number Reflections(All) 35072
    Number Reflections(Observed) 34818
    Percent Possible(Observed) 99.3
    R Merge I(Observed) 0.112
    B(Isotropic) From Wilson Plot 39.239
    Redundancy 5.63
     
    High Resolution Shell Details
    Resolution(High) 2.16
    Resolution(Low) 2.29
    Percent Possible(All) 96.0
    R Merge I(Observed) 0.696
    Mean I Over Sigma(Observed) 2.6
    R-Sym I(Observed) 0.698
    Redundancy 5.46
    Number Unique Reflections(All) 5614
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.16
    Resolution(Low) 47.262
    Cut-off Sigma(I) -3.0
    Cut-off Sigma(F) 2.0
    Number of Reflections(all) 34818
    Number of Reflections(Observed) 34809
    Number of Reflections(R-Free) 1740
    Percent Reflections(Observed) 99.25
    R-Factor(Observed) 0.1703
    R-Work 0.1667
    R-Free 0.2407
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 30.24
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1573
    Shell Resolution(Low) 2.2208
    Number of Reflections(Observed) 2507
    Number of Reflections(R-Free) 132
    Number of Reflections(R-Work) 2507
    R-Factor(R-Work) 0.225
    R-Factor(R-Free) 0.3442
    Percent Reflections(Observed) 92.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2208
    Shell Resolution(Low) 2.2925
    Number of Reflections(Observed) 2787
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2787
    R-Factor(R-Work) 0.2225
    R-Factor(R-Free) 0.305
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2925
    Shell Resolution(Low) 2.3744
    Number of Reflections(Observed) 2757
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2757
    R-Factor(R-Work) 0.2082
    R-Factor(R-Free) 0.2895
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3744
    Shell Resolution(Low) 2.4695
    Number of Reflections(Observed) 2769
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2769
    R-Factor(R-Work) 0.196
    R-Factor(R-Free) 0.3151
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4695
    Shell Resolution(Low) 2.5819
    Number of Reflections(Observed) 2752
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2752
    R-Factor(R-Work) 0.1906
    R-Factor(R-Free) 0.2724
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5819
    Shell Resolution(Low) 2.718
    Number of Reflections(Observed) 2789
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2789
    R-Factor(R-Work) 0.1872
    R-Factor(R-Free) 0.2512
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.718
    Shell Resolution(Low) 2.8883
    Number of Reflections(Observed) 2755
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2755
    R-Factor(R-Work) 0.1813
    R-Factor(R-Free) 0.2964
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.8883
    Shell Resolution(Low) 3.1112
    Number of Reflections(Observed) 2775
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2775
    R-Factor(R-Work) 0.1872
    R-Factor(R-Free) 0.2781
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1112
    Shell Resolution(Low) 3.4242
    Number of Reflections(Observed) 2798
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2798
    R-Factor(R-Work) 0.1675
    R-Factor(R-Free) 0.2528
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.4242
    Shell Resolution(Low) 3.9195
    Number of Reflections(Observed) 2769
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2769
    R-Factor(R-Work) 0.143
    R-Factor(R-Free) 0.19
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9195
    Shell Resolution(Low) 4.9374
    Number of Reflections(Observed) 2787
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2787
    R-Factor(R-Work) 0.1266
    R-Factor(R-Free) 0.2023
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.9374
    Shell Resolution(Low) 47.2737
    Number of Reflections(Observed) 2824
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2824
    R-Factor(R-Work) 0.1566
    R-Factor(R-Free) 0.1964
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.018
    f_chiral_restr 0.07
    f_dihedral_angle_d 16.194
    f_angle_d 1.104
    f_bond_d 0.008
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 4965
    Nucleic Acid Atoms 0
    Heterogen Atoms 196
    Solvent Atoms 274
     
     
  •   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