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Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate zinc-chelator water-soluble inhibitor (DC28).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IOL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Protein-ligand: 465 micro-M hMMP12 F171D E219Q, 0.020 M acetohydroxamic acid, 10% DMSO, 0.5 milli-M inhibitor (DC28).
Precipitant: 40.5% PEG4K, 10% dioxane, 2% ethylene glycol, 0.18 M imidazole piperidine, pH 8.5.
Cryoprotectant:40% cryomix CM12: (,25 % diethylene glycol + 12.5 % glycerol + 25 % 1,2-propanediol + 12.5 % 1,4-dioxane), 25% PEG 6K, 0.1 M TRIS HCl, pH 8.0.
Crystal Properties Matthews coefficient Solvent content 2.22 44.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.98 α = 90 b = 63.51 β = 102.31 c = 78.64 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 CCD ADSC QUANTUM 315r mirrors 2014-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 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 1.95 44.56 98.4 0.23 0.21 4.79 4.49 45133 -3 24.46
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 1.95 2 86.8 0.985 1.68 4.25
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5IOL 2.05 32.87 36421 1917 98.6 0.212 0.21 0.2112 0.249 0.2491 RANDOM 30
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] -0.18 0.16 -0.24 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.186 r_dihedral_angle_4_deg 21.241 r_dihedral_angle_3_deg 15.284 r_long_range_B_refined 8.274 r_dihedral_angle_1_deg 6.89 r_mcangle_it 4.344 r_scbond_it 3.833 r_mcbond_it 3.05 r_angle_refined_deg 1.938 r_chiral_restr 0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.186 r_dihedral_angle_4_deg 21.241 r_dihedral_angle_3_deg 15.284 r_long_range_B_refined 8.274 r_dihedral_angle_1_deg 6.89 r_mcangle_it 4.344 r_scbond_it 3.833 r_mcbond_it 3.05 r_angle_refined_deg 1.938 r_chiral_restr 0.159 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5080 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building