☰ Navigation Tabs
Crystal structure of the catalytic domain of MMP-12 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 4H84
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Protein-inhibitor complex: hMMP12 0.631 milli-M + 0.010 M Acetohydroxamic acid + 0.005 M inhibitor DC27, 10% DMSO.
precipitant: 34% PEG 4K, 1.5 M imidazole piperidine, pH 8.5, Dioxane 25%
Cryoprotectant: 40% Cryomix: (12.5 % diethylene glycol + 12.5 % glycerol + 12.5 % 1,2-propanediol + 12.5 % 2,3-butanediol + 25 % DMSO + 30 % 1,4-dioxane), 25% MPEG 6K, 0.1 M AAB (Na acetate, ADA, Bicine: 10% acid/90% basic), pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.15 42.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.09 α = 90 b = 62.86 β = 102.54 c = 63.75 γ = 90
Symmetry Space Group P 1 21 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 6M Mirrors 2015-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965 ESRF MASSIF-1
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 2.45 45 99.2 0.111 0.093 9.6 3.14 11195 -3 28.91
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 2.45 2.51 99.3 0.23 5.23 3.23
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 4H84 2.45 44.22 1.05 11075 555 99 0.179 0.175 0.179 0.253 0.2439
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 18.48 f_angle_d 1.754 f_chiral_restr 0.123 f_bond_d 0.015 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2484 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 142
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling REFMAC phasing Coot model building