6EOX

Crystal structure of MMP12 in complex with carboxylic inhibitor LP165.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H76 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293Drop: 1 micro-L (hMMP-12 at 855 micro-M + 1 milli-M hydroxamic acid + 1 milli-M LP165) and 1 micro-L reservoir solution. Precipitant: 17% PEG 20K, 0.2M imidazole malate 250mM NaCl, pH 8.5. Cryoprotection: 40% MPEG 5K, 10% 1,2-propanediol, 10% AAB (sodium acetate, ADA, bicine: 90% basic/10% acid), pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.1141.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.16α = 90
b = 59.86β = 115.73
c = 53.94γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2nd mirror Zerodur with Pt coating2010-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.979696ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.34979.70.99914.424.1428894-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3831.81.310.3431.023.68

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4H761.348.5926772199679.70.1450.1420.179RANDOM18.43
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]
0.4-0.06-0.390.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.86
r_sphericity_free21.923
r_dihedral_angle_4_deg18.752
r_dihedral_angle_3_deg13.302
r_sphericity_bonded7.583
r_rigid_bond_restr6.98
r_dihedral_angle_1_deg5.775
r_long_range_B_refined3.854
r_long_range_B_other3.597
r_scangle_other3.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.86
r_sphericity_free21.923
r_dihedral_angle_4_deg18.752
r_dihedral_angle_3_deg13.302
r_sphericity_bonded7.583
r_rigid_bond_restr6.98
r_dihedral_angle_1_deg5.775
r_long_range_B_refined3.854
r_long_range_B_other3.597
r_scangle_other3.312
r_scbond_it2.9
r_scbond_other2.899
r_mcangle_it2.481
r_mcangle_other2.481
r_mcbond_it2.147
r_mcbond_other2.135
r_angle_other_deg1.936
r_angle_refined_deg1.649
r_chiral_restr0.113
r_bond_refined_d0.072
r_gen_planes_refined0.011
r_gen_planes_other0.004
r_bond_other_d0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1238
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building