5CZM

Crystal structure of a mutated catalytic domain of Human MMP12 in complex with 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 : MMP12h F67D K241A 850 micro-M + 10mM AHA Drop : 1 micro-L protein + 0.35 micro-l inhibitor(1.5 milli-M, DMSO) Precipitant : 20% PEG4K, 0.2 M TRIS pH9.5 Cryo protectant : 5% diethylene glycol, 0% ethylene glycol, 5% MPD + 5% glycerol, 5% 2,3-butanediol, 5mM NDSB 201, 25% PEG 6K, 100mM TRIS HCl, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.2344.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.97α = 90
b = 63.29β = 90
c = 35.91γ = 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)2015-07-12MSINGLE 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
11.346.63299.60.2070.1919.966.57432574004-3
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)
11.31.3897.52.0971.16.14

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 REPLACEMENTTHROUGHOUT4GQL1.30328.4511.3439081195499.720.14680.14540.1739RANDOM
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_d14.101
f_angle_d1.057
f_chiral_restr0.07
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1242
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms57

Software

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