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Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated thiourea-linked carboxylate zinc-chelator water-soluble inhibitor (DC31).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Protein-ligand: hMMP12 F67D E219Q 465 micro-M, 0.02M acetohydroxamic acid 0.5 milli-M inhibitor (DC31) 10% DMSO.
Precipitant: 32.4% PEG 4K, 8% dioxane, 0.2M imidazole piperidine, pH 8.5.
Cryoprotectant:
40% cryomix:(12.5 % diethylene glycol + 12.5 % glycerol + 12.5 % 1,2-propanediol + 25 % DMSO + 25 % 1,4-dioxane) 12% PEG 4K, 10% Dioxane, 0.1 M imidazole piperidine pH 8.5.
Crystal Properties Matthews coefficient Solvent content 2.19 43.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.72 α = 90 b = 63.14 β = 103.09 c = 78.92 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 2015-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 2.17 48.79 99.3 0.1 0.096 0.997 9.44 4.34 32560 -3 33.956
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 2.17 2.23 98.9 0.523 3.06 3.73
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5I2Z 2.17 48.79 30719 1617 99.36 0.2085 0.20615 0.25324 0.256 RANDOM 36.572
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] -1.53 0.98 -3.8 4.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.216 r_dihedral_angle_4_deg 17.818 r_dihedral_angle_3_deg 12.398 r_long_range_B_refined 8.183 r_long_range_B_other 8.023 r_dihedral_angle_1_deg 6.907 r_scangle_other 5.652 r_mcangle_other 4.229 r_mcangle_it 4.228 r_scbond_it 3.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.216 r_dihedral_angle_4_deg 17.818 r_dihedral_angle_3_deg 12.398 r_long_range_B_refined 8.183 r_long_range_B_other 8.023 r_dihedral_angle_1_deg 6.907 r_scangle_other 5.652 r_mcangle_other 4.229 r_mcangle_it 4.228 r_scbond_it 3.68 r_scbond_other 3.679 r_mcbond_it 2.939 r_mcbond_other 2.938 r_angle_refined_deg 1.904 r_angle_other_deg 1.054 r_chiral_restr 0.116 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.004 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4936 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing PHENIX refinement Coot model building