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Crystal structure of the catalytic domain of MMP-9 in complex with a selective sugar-conjugated arylsulfonamide carboxylate water-soluble inhibitor (DC27).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.25 293 protein solution: 415.2 micro-M MMP9 WT + 0.120 M Acetohydroxamic acid in 20 mM Tris pH 7.0 with 0.001 M inhibitor DC27 and 10% DMSO.
precipitant: 40% MPEG 5K ; 0.1 M bicine ; pH 7.25
sitting drops of 1 micro-L protein solution and 1 micro-L precipitant solution.
cryoprotectant:_40% cryomix CM2 (25 % di-ethylene glycol + 25 % glycerol + 25 % 1,2-propanediol), 10% PEG 10K, 200 milli-M NaCl, 100 milli-M Na propionate, Na cacodylate, Bis-Tris-propane (PCTP 50% acid/50% basic) pH 7.0 + 0.001 M inhibitor DC27.
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.56 α = 90 b = 39.56 β = 90 c = 163.55 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M mirrors 2014-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.59 35 99.7 0.115 0.111 15.04 13.2 20981 -3 27.18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.63 96.8 1.63 1.65 13.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4H3X 1.59 34.26 1.36 20929 1047 99.7 0.19 0.188 0.1904 0.228 0.2311
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.884 f_angle_d 1.033 f_chiral_restr 0.044 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1249 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 71
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building