3TVC

Human MMP13 in complex with L-glutamate motif inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QJ23QJ2 catalytic domain only (Chain A)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5293PROTEIN-INHIBITOR SOLUTION: MMP13 AT 20 MG/ML CO-CRYSTALLIZED WITH E3P AT 1.1 MILLI-M. RESERVOIR SOLUTION: 17.5% PEG 20K, 0.1 M MES, 0.02 M NACL. CRYOPROTECTANT: 5% DIETHYLENE GLYCOL, 5% ETHYLENE GLYCOL, 5% MPD, 5% PROPYLENE GLYCOL, 5% DMSO, 5% GLYCEROL, 0.005 M 3-(-PYRIDINIO)-1-PROPANESULFONATE, 10% PEG 20K, 0.033 M SODIUM ACETATE, 0.033 M ADA, 0.033 M BICINE, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.7655.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.303α = 90
b = 85.16β = 90
c = 40.916γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rbent cylindrical mirror2011-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.972420ESRFID23-1

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
12.4385.196.90.290.3110.67.218412815135.49
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.432.5987.41.3991.292.816.631231

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3QJ2 catalytic domain only (Chain A)2.4340.9161.348377812736997.020.16540.16220.2341RANDOM24.782
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]
-2.75431.25481.4995
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d21.949
f_angle_d1.121
f_chiral_restr0.083
f_bond_d0.008
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1347
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms58

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling