5D2B

Crystal structure of a mutated 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 : hMMP12 F171D at 820 micro-M + 10 milli-M AHA + 0.708 milli-M inhibitor. Precipitant : 20% PEG4000, 0.2 M TRIS pH 9.5 Cryoprotectant : 10 % diethylene glycol + 5 % glycerol + 10 % 1,2-propanediol + 5 % 1,4-dioxane + 25% PEG6000 + 0.1 M TRIS HCl pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.2745.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.9α = 90
b = 63.1β = 90
c = 36.79γ = 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 20.9184SOLEILPROXIMA 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
11.232.45399.60.10.0898.784.69696696542-3
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)
11.21.2396.91.051.532.9

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 REPLACEMENTTHROUGHOUT4GQL1.232.453196507481599.530.15540.15440.1747Random
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_d14.719
f_angle_d1.067
f_chiral_restr0.07
f_plane_restr0.006
f_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1246
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms51

Software

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