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X-RAY DIFFRACTION
Materials and Methods page
4H76
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 293.0
    Details Protein:(hMMP12 F171D at 927 micro-M + acetohydroxamic acid at 11.6 milli-M Reservoir: 45% PEG 4,000 0.2 M imidazole piperidine Cryoprotection: 10% Di-ethylene glycol, 10% 1.2-propanediol, 10% glycerol, 10% PEG 10,000, 10% (AAB buffer 10% acid/90% basic) 0.2 M NaCl. Flash cooling in LN2. , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 69.92 α = 90
    b = 62.89 β = 90
    c = 37.7 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 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) 1.5
    Resolution(Low) 50
    Number Reflections(All) 27511
    Number Reflections(Observed) 27420
    Percent Possible(Observed) 99.7
    R Merge I(Observed) 0.114
    B(Isotropic) From Wilson Plot 21.127
    Redundancy 7.98
     
    High Resolution Shell Details
    Resolution(High) 1.5
    Resolution(Low) 1.59
    R Merge I(Observed) 1.094
    Mean I Over Sigma(Observed) 2.5
    R-Sym I(Observed) 0.982
    Redundancy 7.92
    Number Unique Reflections(All) 4379
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.5
    Resolution(Low) 46.758
    Cut-off Sigma(I) -3.0
    Cut-off Sigma(F) 2.0
    Number of Reflections(all) 27420
    Number of Reflections(Observed) 27413
    Number of Reflections(R-Free) 1371
    Percent Reflections(Observed) 99.63
    R-Factor(Observed) 0.1662
    R-Work 0.165
    R-Free 0.1884
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 12.02
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.4969
    Shell Resolution(Low) 1.5504
    Number of Reflections(Observed) 2477
    Number of Reflections(R-Free) 130
    Number of Reflections(R-Work) 2477
    R-Factor(R-Work) 0.2284
    R-Factor(R-Free) 0.2341
    Percent Reflections(Observed) 97.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.5504
    Shell Resolution(Low) 1.6125
    Number of Reflections(Observed) 2575
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2575
    R-Factor(R-Work) 0.204
    R-Factor(R-Free) 0.2207
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6125
    Shell Resolution(Low) 1.6859
    Number of Reflections(Observed) 2571
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2571
    R-Factor(R-Work) 0.1866
    R-Factor(R-Free) 0.2466
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.6859
    Shell Resolution(Low) 1.7747
    Number of Reflections(Observed) 2593
    Number of Reflections(R-Free) 136
    Number of Reflections(R-Work) 2593
    R-Factor(R-Work) 0.1708
    R-Factor(R-Free) 0.2135
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.7747
    Shell Resolution(Low) 1.8859
    Number of Reflections(Observed) 2590
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2590
    R-Factor(R-Work) 0.1651
    R-Factor(R-Free) 0.1725
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.8859
    Shell Resolution(Low) 2.0316
    Number of Reflections(Observed) 2575
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2575
    R-Factor(R-Work) 0.1515
    R-Factor(R-Free) 0.1909
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0316
    Shell Resolution(Low) 2.236
    Number of Reflections(Observed) 2609
    Number of Reflections(R-Free) 138
    Number of Reflections(R-Work) 2609
    R-Factor(R-Work) 0.1564
    R-Factor(R-Free) 0.1673
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.236
    Shell Resolution(Low) 2.5595
    Number of Reflections(Observed) 2616
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2616
    R-Factor(R-Work) 0.1669
    R-Factor(R-Free) 0.203
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5595
    Shell Resolution(Low) 3.2246
    Number of Reflections(Observed) 2651
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2651
    R-Factor(R-Work) 0.1612
    R-Factor(R-Free) 0.1837
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2246
    Shell Resolution(Low) 46.7812
    Number of Reflections(Observed) 2785
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2785
    R-Factor(R-Work) 0.1542
    R-Factor(R-Free) 0.1706
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.005
    f_chiral_restr 0.076
    f_dihedral_angle_d 16.441
    f_angle_d 1.079
    f_bond_d 0.007
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1246
    Nucleic Acid Atoms 0
    Heterogen Atoms 72
    Solvent Atoms 201
     
     
  •   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