5I43

Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate chelator water-soluble inhibitor (DC32).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5I3M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5295Protein-ligand: hMMP12 F171D E219Q 465 micro-M in 0.020 M Tris-HCl, 3 milli-M CaCl2, 0.2 M NaCl, 0.02 M acetohydroxamic acid, 10% DMSO, pH 7.5, 0.5 milli-M inhibitor (DC31). Precipitant: 40% PEG4K, 9% dioxane, 0.18 M imidazole piperidine, pH 8.5. Cryoprotectant: 40% cryomix SM2:(12.5 % ethylene glycol + 12.5 % glycerol + 12.5 % 1,2-propanediol + 25 % DMSO + 37.5 % 1,4-dioxane), 22.5% MPEG 4K, 5% dioxane, 100 mM imidazole piperidine pH 8.5.
Crystal Properties
Matthews coefficientSolvent content
2.244.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.03α = 90
b = 63.66β = 103.03
c = 79.03γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6Mmirrors2015-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.97857SOLEILPROXIMA 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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9544.5699.90.1720.1670.9937.245.9745366-326.387
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.95299.80.7162.023.96

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5I3M1.9544.5643013226499.830.202050.200390.23323RANDOM27.062
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]
-1.320.39-1.682.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.101
r_dihedral_angle_4_deg20.364
r_dihedral_angle_3_deg13.61
r_long_range_B_refined8.399
r_long_range_B_other8.177
r_dihedral_angle_1_deg7.085
r_scangle_other5.515
r_scbond_it3.604
r_scbond_other3.603
r_mcangle_other3.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.101
r_dihedral_angle_4_deg20.364
r_dihedral_angle_3_deg13.61
r_long_range_B_refined8.399
r_long_range_B_other8.177
r_dihedral_angle_1_deg7.085
r_scangle_other5.515
r_scbond_it3.604
r_scbond_other3.603
r_mcangle_other3.45
r_mcangle_it3.449
r_mcbond_it2.367
r_mcbond_other2.364
r_angle_refined_deg1.989
r_angle_other_deg1.073
r_chiral_restr0.119
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.004
r_gen_planes_other0.003
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 AtomsNumber
Protein Atoms5124
Nucleic Acid Atoms
Solvent Atoms595
Heterogen Atoms206

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building