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X-RAY DIFFRACTION
Materials and Methods page
4I03
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, SITTING DROP
    pH 8.5
    Temperature 293.0
    Details Protein solution: 222 microM MMP12 mutant E219A 106 microM bifunctional inhibitor LD884. Reservoir: 27% PEG 10K, 150mM imidazole piperidine, pH 8.5. Cryoprotectant: 5 % di-ethylene glycol + 5 % ethylene glycol + 10 % 1,2-propanediol + 5 % DMSO + 5 % glycerol, 25% MPEG 5K, 100mM (Na acetate, ADA, Bicine 10% pH 4.0/90% pH 9.0), VAPOR DIFFUSION, SITTING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 51.79 α = 90
    b = 60.1 β = 116.67
    c = 54.92 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector PIXEL
    Type PSI PILATUS 6M
    Details mirrors
    Collection Date 2012-10-12
     
    Diffraction Radiation
    Monochromator SAGITALLY FOCUSED Si(111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type SOLEIL BEAMLINE PROXIMA 1
    Wavelength List 0.980110
    Site SOLEIL
    Beamline PROXIMA 1
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -4.0
    Resolution(High) 1.7
    Resolution(Low) 50
    Number Reflections(All) 16789
    Number Reflections(Observed) 16663
    Percent Possible(Observed) 99.2
    R Merge I(Observed) 0.102
    B(Isotropic) From Wilson Plot 28.35
    Redundancy 4.14
     
    High Resolution Shell Details
    Resolution(High) 1.7
    Resolution(Low) 1.8
    Percent Possible(All) 97.2
    R Merge I(Observed) 0.887
    Mean I Over Sigma(Observed) 1.71
    R-Sym I(Observed) 0.768
    Redundancy 4.02
    Number Unique Reflections(All) 2693
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 1.7
    Resolution(Low) 36.67
    Cut-off Sigma(I) -4.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 16663
    Number of Reflections(Observed) 15828
    Number of Reflections(R-Free) 834
    Percent Reflections(Observed) 100.0
    R-Factor(Observed) 0.14626
    R-Work 0.14361
    R-Free 0.19397
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model Isotropic
    Mean Isotropic B Value 19.56
    Anisotropic B[1][1] 0.05
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.06
    Anisotropic B[2][2] -0.05
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 0.05
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.696
    Shell Resolution(Low) 1.74
    Number of Reflections(R-Free) 60
    Number of Reflections(R-Work) 1124
    R-Factor(R-Work) 0.252
    R-Factor(R-Free) 0.296
    Percent Reflections(Observed) 100.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_scangle_it 4.865
    r_scbond_it 3.131
    r_mcangle_it 2.29
    r_mcbond_other 0.414
    r_bond_refined_d 0.022
    r_bond_other_d 0.002
    r_angle_refined_deg 2.038
    r_angle_other_deg 1.033
    r_dihedral_angle_1_deg 7.055
    r_dihedral_angle_2_deg 35.842
    r_dihedral_angle_3_deg 16.634
    r_dihedral_angle_4_deg 18.651
    r_chiral_restr 0.114
    r_gen_planes_refined 0.011
    r_gen_planes_other 0.003
    r_mcbond_it 1.372
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 1242
    Nucleic Acid Atoms 0
    Heterogen Atoms 139
    Solvent Atoms 171
     
     
  •   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