4XCT

Crystal structure of a hydroxamate based inhibitor ARP101 (EN73) in complex with the MMP-9 catalytic domain.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293protein: hMMP-9-WT at 337 micro-M with 120 milli-M acetohydroxamic acid. precipitant: 40.5% MPEG 5,000, 180 mM imidazole piperidine, pH 8.5. Cryoprotectant: 40% CryoProtX-C1, 10% PEG 10K, 10% PCTP 50/50
Crystal Properties
Matthews coefficientSolvent content
2.0740.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.6α = 90
b = 39.6β = 90
c = 163.96γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6Mmirrors2014-12-16MSINGLE 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)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
11.35299.80.060.05514.626.23809638007-3
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)
11.31.3899.11.3921.126.16

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4H3X1.334.2951.3637897189299.70.17010.16680.231Random selection
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_d14.462
f_angle_d1.049
f_chiral_restr0.053
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1277
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms51

Software

Software
Software NamePurpose
PHENIXrefinement
MOLREPphasing
XDSdata reduction
Cootmodel building
XSCALEdata scaling