4HMA

Crystal structure of an MMP twin carboxylate based inhibitor LC20 in complex with the MMP-9 catalytic domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H82 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6293Protein: human MMP9 (E402Q) at 308.7 micro-M twin inhibitor LC20 at 154 micro-M (stoichiometry 2:1) and 120mM acetohydroxamic acid. RESERVOIR: 12% Polyethylene glycol 20,000, 1.5M NaCl, 0.1 M PCTP (Na propionate, Na cacodylate, Bis-Tris-propane ratio 2:1:2; 75% pH 4, 25% pH 9.5) CRYOPROTECTANT: 40% C2 (25 % di-ethylene glycol + 25 % glycerol + 25 % 1,2-propanediol), 9% PEG 10,000 1.5M NaCl, 0.1M PCTP 80/2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.448.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.87α = 90
b = 98.24β = 90
c = 47.44γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6Mbent cylindrical mirror2012-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.98011SOLEILPROXIMA 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
11.945099.40.1660.1558.197.982617326019-336.556
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)
11.942.0696.61.5331.4321.37.874162

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUT4H821.9442.72-3260192471313011000.214390.210880.28302RANDOM32.048
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]
0.82-0.65-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.336
r_dihedral_angle_4_deg24.017
r_dihedral_angle_3_deg16.531
r_dihedral_angle_1_deg6.74
r_scangle_it4.572
r_scbond_it3.114
r_mcangle_it2.12
r_angle_refined_deg1.966
r_mcbond_it1.241
r_chiral_restr0.158
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.336
r_dihedral_angle_4_deg24.017
r_dihedral_angle_3_deg16.531
r_dihedral_angle_1_deg6.74
r_scangle_it4.572
r_scbond_it3.114
r_mcangle_it2.12
r_angle_refined_deg1.966
r_mcbond_it1.241
r_chiral_restr0.158
r_bond_refined_d0.022
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2550
Nucleic Acid Atoms
Solvent Atoms345
Heterogen Atoms190

Software

Software
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling