5D3C

Crystal structure of a double mutant catalytic domain of Human MMP12 in complex with an hydroxamate analogue of RXP470


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.5293Protein : MMP12 F67D K241A, 1 mili-M + 10 mili-M AHA Drop : 1 micro-L protein + 0.2 micro-L inhibitor (5 mili-M in DMSO) Precipitant : 20% PEG4000, 0.2 M TRIS pH 9.5 Cryoprotectant : 10 % diethylene glycol + 5 % glycerol + 10 % 2,3-butanediol + 5 % 1,4-dioxane +25% PEG6000,+ 100 mili-M TRIS HCl, pH 8.
Crystal Properties
Matthews coefficientSolvent content
2.2545.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.64α = 90
b = 63.06β = 90
c = 36.54γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rconvex horizontal pre-focussing mirror (HPM) and a pair of focusing bimorph mirrors in Kirkpatrick-Baez (KB) configuration2015-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.9801SOLEILPROXIMA 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
11.3146.43897.60.1230.1219.476.837296971186-3
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)
11.311.3573.21.641.033.93

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 REPLACEMENTTHROUGHOUT4GQL1.31446.4381.2271174355797.540.15450.15260.1913Random
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_d12.42
f_angle_d1.071
f_chiral_restr0.071
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1242
Nucleic Acid Atoms
Solvent Atoms274
Heterogen Atoms51

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
MxCuBEdata collection