5I12

Crystal structure of the catalytic domain of MMP-9 in complex with a selective sugar-conjugated arylsulfonamide carboxylate water-soluble inhibitor (DC27).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H3X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.25293protein 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 coefficientSolvent content
2.141.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.56α = 90
b = 39.56β = 90
c = 163.55γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2Mmirrors2014-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8729ESRFID23-2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.593599.70.1150.11115.0413.220981-327.18
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)
11.591.6396.81.631.6513.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4H3X1.5934.261.3620929104799.70.190.1880.228
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.884
f_angle_d1.033
f_chiral_restr0.044
f_bond_d0.006
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1249
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms71

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building