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X-RAY DIFFRACTION
Materials and Methods page
4H84
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 293.0
    Details Protein: hMMP12 F171D at4 784 mico-M + 10 milli-M AHA Reservoir: 12% PEG 20K, 0.14 M imidazole malate, .0175 M NaCl Cryoprotectant: 40% C7 (C7 = 12.5 % di-ethylene glycol + 12.5 % ethylene glycol + 25 % 1,2-propanediol + 12.5 % DMSO + 12.5 % glycerol), 1M NaCl, 0.1 M (MMT buffer 75% acid/25% basic), 9% PEG 10.000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 42.14 α = 90
    b = 62.79 β = 90
    c = 113.14 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 CCD
    Type ADSC QUANTUM 315r
    Details MIRRORS
    Collection Date 2012-06-14
     
    Diffraction Radiation
    Monochromator Single Silicon (111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type ESRF BEAMLINE ID23-1
    Wavelength List 0.9763
    Site ESRF
    Beamline ID23-1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.59
    Resolution(Low) 50
    Number Reflections(All) 41050
    Number Reflections(Observed) 40489
    Percent Possible(Observed) 98.6
    R Merge I(Observed) 0.159
    B(Isotropic) From Wilson Plot 21.449
    Redundancy 7.68
     
    High Resolution Shell Details
    Resolution(High) 1.59
    Resolution(Low) 1.69
    Percent Possible(All) 92.6
    R Merge I(Observed) 0.957
    Mean I Over Sigma(Observed) 3.13
    R-Sym I(Observed) 0.892
    Redundancy 7.47
    Number Unique Reflections(All) 6540
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.592
    Resolution(Low) 42.029
    Cut-off Sigma(I) -3.0
    Cut-off Sigma(F) 2.02
    Number of Reflections(all) 40489
    Number of Reflections(Observed) 40486
    Number of Reflections(R-Free) 2024
    Percent Reflections(Observed) 98.64
    R-Factor(Observed) 0.1729
    R-Work 0.1711
    R-Free 0.2062
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 21.4
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5924
    Shell Resolution(Low) 1.6323
    Number of Reflections(Observed) 2270
    Number of Reflections(R-Free) 120
    Number of Reflections(R-Work) 2270
    R-Factor(R-Work) 0.2899
    R-Factor(R-Free) 0.3273
    Percent Reflections(Observed) 83.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6323
    Shell Resolution(Low) 1.6764
    Number of Reflections(Observed) 2774
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2774
    R-Factor(R-Work) 0.2288
    R-Factor(R-Free) 0.2873
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6764
    Shell Resolution(Low) 1.7257
    Number of Reflections(Observed) 2727
    Number of Reflections(R-Free) 143
    Number of Reflections(R-Work) 2727
    R-Factor(R-Work) 0.2056
    R-Factor(R-Free) 0.2576
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7257
    Shell Resolution(Low) 1.7814
    Number of Reflections(Observed) 2742
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2742
    R-Factor(R-Work) 0.1915
    R-Factor(R-Free) 0.2474
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7814
    Shell Resolution(Low) 1.8451
    Number of Reflections(Observed) 2770
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2770
    R-Factor(R-Work) 0.1808
    R-Factor(R-Free) 0.2029
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8451
    Shell Resolution(Low) 1.919
    Number of Reflections(Observed) 2748
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2748
    R-Factor(R-Work) 0.176
    R-Factor(R-Free) 0.2114
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.919
    Shell Resolution(Low) 2.0063
    Number of Reflections(Observed) 2752
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2752
    R-Factor(R-Work) 0.1726
    R-Factor(R-Free) 0.1938
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0063
    Shell Resolution(Low) 2.1121
    Number of Reflections(Observed) 2774
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2774
    R-Factor(R-Work) 0.1648
    R-Factor(R-Free) 0.234
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1121
    Shell Resolution(Low) 2.2444
    Number of Reflections(Observed) 2756
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2756
    R-Factor(R-Work) 0.1672
    R-Factor(R-Free) 0.2075
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2444
    Shell Resolution(Low) 2.4177
    Number of Reflections(Observed) 2779
    Number of Reflections(R-Free) 146
    Number of Reflections(R-Work) 2779
    R-Factor(R-Work) 0.1671
    R-Factor(R-Free) 0.2229
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4177
    Shell Resolution(Low) 2.6609
    Number of Reflections(Observed) 2797
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2797
    R-Factor(R-Work) 0.1627
    R-Factor(R-Free) 0.1844
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.6609
    Shell Resolution(Low) 3.0459
    Number of Reflections(Observed) 2802
    Number of Reflections(R-Free) 148
    Number of Reflections(R-Work) 2802
    R-Factor(R-Work) 0.1618
    R-Factor(R-Free) 0.2028
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.0459
    Shell Resolution(Low) 3.8371
    Number of Reflections(Observed) 2859
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2859
    R-Factor(R-Work) 0.1484
    R-Factor(R-Free) 0.1817
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.8371
    Shell Resolution(Low) 42.0431
    Number of Reflections(Observed) 2912
    Number of Reflections(R-Free) 153
    Number of Reflections(R-Work) 2912
    R-Factor(R-Work) 0.1612
    R-Factor(R-Free) 0.1748
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.006
    f_chiral_restr 0.167
    f_dihedral_angle_d 16.957
    f_angle_d 1.262
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2492
    Nucleic Acid Atoms 0
    Heterogen Atoms 181
    Solvent Atoms 273
     
     
  •   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