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X-RAY DIFFRACTION
Materials and Methods page
4H30
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 293.0
    Details Protein: hMMP12 F171D at 0.36 milli-M + 0.001 M AHA. Reservoir: 13% PEG 20,000 0.2 M imidazole malate 0.05 M NaCl Cryoprotectant: 27% PEG 8,000 15% MPEG 550, 10% glycerol, 0.09 M Tris-HCl , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 46.91 α = 90
    b = 61.75 β = 90
    c = 112.56 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 21
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type DECTRIS PILATUS 6M
    Details mirrors
    Collection Date 2012-05-01
     
    Diffraction Radiation
    Monochromator Si 111 CHANNEL
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SOLEIL BEAMLINE PROXIMA 1
    Wavelength List 0.8856
    Site SOLEIL
    Beamline PROXIMA 1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.43
    Resolution(Low) 50
    Number Reflections(All) 61962
    Number Reflections(Observed) 61752
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.059
    B(Isotropic) From Wilson Plot 21.616
    Redundancy 5.82
     
    High Resolution Shell Details
    Resolution(High) 1.42
    Resolution(Low) 1.51
    Percent Possible(All) 98.4
    R Merge I(Observed) 0.626
    Mean I Over Sigma(Observed) 2.77
    R-Sym I(Observed) 0.57
    Redundancy 5.8
    Number Unique Reflections(All) 9880
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.43
    Resolution(Low) 43.31
    Cut-off Sigma(I) -3.0
    Cut-off Sigma(F) 1.99
    Number of Reflections(all) 61752
    Number of Reflections(Observed) 61749
    Number of Reflections(R-Free) 3087
    Percent Reflections(Observed) 99.66
    R-Factor(Observed) 0.1577
    R-Work 0.1567
    R-Free 0.1767
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4244
    Shell Resolution(Low) 1.4467
    Number of Reflections(Observed) 2460
    Number of Reflections(R-Free) 129
    Number of Reflections(R-Work) 2460
    R-Factor(R-Work) 0.227
    R-Factor(R-Free) 0.223
    Percent Reflections(Observed) 94.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4467
    Shell Resolution(Low) 1.4704
    Number of Reflections(Observed) 2675
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2675
    R-Factor(R-Work) 0.2062
    R-Factor(R-Free) 0.2565
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4704
    Shell Resolution(Low) 1.4958
    Number of Reflections(Observed) 2628
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2628
    R-Factor(R-Work) 0.1968
    R-Factor(R-Free) 0.2057
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4958
    Shell Resolution(Low) 1.523
    Number of Reflections(Observed) 2642
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2642
    R-Factor(R-Work) 0.1857
    R-Factor(R-Free) 0.2159
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.523
    Shell Resolution(Low) 1.5523
    Number of Reflections(Observed) 2639
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2639
    R-Factor(R-Work) 0.1799
    R-Factor(R-Free) 0.2021
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5523
    Shell Resolution(Low) 1.584
    Number of Reflections(Observed) 2665
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2665
    R-Factor(R-Work) 0.1702
    R-Factor(R-Free) 0.2023
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.584
    Shell Resolution(Low) 1.6184
    Number of Reflections(Observed) 2636
    Number of Reflections(R-Free) 139
    Number of Reflections(R-Work) 2636
    R-Factor(R-Work) 0.1667
    R-Factor(R-Free) 0.212
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6184
    Shell Resolution(Low) 1.6561
    Number of Reflections(Observed) 2630
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2630
    R-Factor(R-Work) 0.1642
    R-Factor(R-Free) 0.1744
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6561
    Shell Resolution(Low) 1.6975
    Number of Reflections(Observed) 2615
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2615
    R-Factor(R-Work) 0.16
    R-Factor(R-Free) 0.2138
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6975
    Shell Resolution(Low) 1.7434
    Number of Reflections(Observed) 2673
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.1571
    R-Factor(R-Free) 0.189
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7434
    Shell Resolution(Low) 1.7947
    Number of Reflections(Observed) 2663
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2663
    R-Factor(R-Work) 0.1555
    R-Factor(R-Free) 0.1849
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7947
    Shell Resolution(Low) 1.8526
    Number of Reflections(Observed) 2652
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2652
    R-Factor(R-Work) 0.1551
    R-Factor(R-Free) 0.1896
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8526
    Shell Resolution(Low) 1.9188
    Number of Reflections(Observed) 2662
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2662
    R-Factor(R-Work) 0.1463
    R-Factor(R-Free) 0.1757
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9188
    Shell Resolution(Low) 1.9956
    Number of Reflections(Observed) 2678
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2678
    R-Factor(R-Work) 0.1487
    R-Factor(R-Free) 0.1632
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.9956
    Shell Resolution(Low) 2.0865
    Number of Reflections(Observed) 2650
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2650
    R-Factor(R-Work) 0.1411
    R-Factor(R-Free) 0.1846
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0865
    Shell Resolution(Low) 2.1965
    Number of Reflections(Observed) 2673
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2673
    R-Factor(R-Work) 0.1441
    R-Factor(R-Free) 0.1709
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1965
    Shell Resolution(Low) 2.3341
    Number of Reflections(Observed) 2692
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2692
    R-Factor(R-Work) 0.1523
    R-Factor(R-Free) 0.1764
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3341
    Shell Resolution(Low) 2.5143
    Number of Reflections(Observed) 2679
    Number of Reflections(R-Free) 141
    Number of Reflections(R-Work) 2679
    R-Factor(R-Work) 0.1566
    R-Factor(R-Free) 0.1812
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5143
    Shell Resolution(Low) 2.7672
    Number of Reflections(Observed) 2719
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2719
    R-Factor(R-Work) 0.1568
    R-Factor(R-Free) 0.1579
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.7672
    Shell Resolution(Low) 3.1676
    Number of Reflections(Observed) 2698
    Number of Reflections(R-Free) 142
    Number of Reflections(R-Work) 2698
    R-Factor(R-Work) 0.1588
    R-Factor(R-Free) 0.1807
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.1676
    Shell Resolution(Low) 3.9904
    Number of Reflections(Observed) 2760
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2760
    R-Factor(R-Work) 0.1405
    R-Factor(R-Free) 0.1629
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.9904
    Shell Resolution(Low) 43.3202
    Number of Reflections(Observed) 2873
    Number of Reflections(R-Free) 151
    Number of Reflections(R-Work) 2873
    R-Factor(R-Work) 0.1613
    R-Factor(R-Free) 0.1585
    Percent Reflections(Observed) 99.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.078
    f_dihedral_angle_d 16.272
    f_angle_d 1.118
    f_bond_d 0.006
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2492
    Nucleic Acid Atoms 0
    Heterogen Atoms 127
    Solvent Atoms 457
     
     
  •   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