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X-RAY DIFFRACTION
Materials and Methods page
4HMA
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 6
    Temperature 293.0
    Details Protein: human MMP9 (E402Q) at 308.7 micro-M twin inhibitor LC20 at 154 micro-M (stoichiometry 2:1) and 120mM acetohydroxamic acid. RESERVOIR: 12% Polyethylene glycol 20,000, 1.5M NaCl, 0.1 M PCTP (Na propionate, Na cacodylate, Bis-Tris-propane ratio 2:1:2; 75% pH 4, 25% pH 9.5) CRYOPROTECTANT: 40% C2 (25 % di-ethylene glycol + 25 % glycerol + 25 % 1,2-propanediol), 9% PEG 10,000 1.5M NaCl, 0.1M PCTP 80/2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 73.87 α = 90
    b = 98.24 β = 90
    c = 47.44 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 FLAT PANEL
    Type PSI PILATUS 6M
    Details bent cylindrical mirror
    Collection Date 2012-10-12
     
    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) 1.94
    Resolution(Low) 50
    Number Reflections(All) 26173
    Number Reflections(Observed) 26019
    Percent Possible(Observed) 99.4
    R Merge I(Observed) 0.166
    B(Isotropic) From Wilson Plot 36.556
    Redundancy 7.98
     
    High Resolution Shell Details
    Resolution(High) 1.94
    Resolution(Low) 2.06
    Percent Possible(All) 96.6
    R Merge I(Observed) 1.533
    Mean I Over Sigma(Observed) 1.3
    R-Sym I(Observed) 1.432
    Redundancy 7.87
    Number Unique Reflections(All) 4162
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.94
    Resolution(Low) 42.72
    Cut-off Sigma(I) -3.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 26019
    Number of Reflections(Observed) 24713
    Number of Reflections(R-Free) 1301
    Percent Reflections(Observed) 100.0
    R-Factor(Observed) 0.21439
    R-Work 0.21088
    R-Free 0.28302
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 32.048
    Anisotropic B[1][1] 0.82
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -0.65
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] -0.18
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.943
    Shell Resolution(Low) 1.993
    Number of Reflections(R-Free) 88
    Number of Reflections(R-Work) 1674
    R-Factor(R-Work) 0.32
    R-Factor(R-Free) 0.373
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.572
    r_scbond_it 3.114
    r_mcangle_it 2.12
    r_mcbond_it 1.241
    r_gen_planes_refined 0.01
    r_chiral_restr 0.158
    r_dihedral_angle_4_deg 24.017
    r_dihedral_angle_3_deg 16.531
    r_dihedral_angle_2_deg 35.336
    r_dihedral_angle_1_deg 6.74
    r_angle_refined_deg 1.966
    r_bond_refined_d 0.022
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2550
    Nucleic Acid Atoms 0
    Heterogen Atoms 190
    Solvent Atoms 345
     
     
  •   Software and Computing Hide
    Computing
    Data Collection DNA
    Data Reduction (intensity integration) XDS
    Data Reduction (data scaling) XDS
    Structure Solution MOLREP
    Structure Refinement REFMAC 5.5.0109
     
    Software
    refinement REFMAC version: 5.5.0109
    model building MOLREP
    data collection DNA