4EFS

Human MMP12 in complex with L-glutamate motif inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LIKPDB entry 3LIK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293Protein solution - 0.53 mM F67D mutant of human MMP12 residues 106-263 in 0.1 M acetohydroxamic acid 0.003 M CaCl2, 0.200 M NaCl 0.02 M Tris-HCl, pH 7.5. Reservoir solution -27% PEG 10K,0.2 M imidazole malate cryoconditions - CryoProtX-Cryomix 7, 25% MPEG 5K, 0.1 M AAB 10/90, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.3246.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.97α = 90
b = 63.19β = 90
c = 37.51γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6Mmirrors2012-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.918400SOLEILPROXIMA 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
11.6346.5997.40.0860.08318.728.72212602071025.023
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)
11.631.7299.30.7260.6833.318.553230

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 DIFFRACTIONRIGID BODYTHROUGHOUTPDB entry 3LIK1.6346.59-3212602006310561000.155540.153680.19044RANDOM20.811
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]
-1.05-0.311.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.385
r_dihedral_angle_4_deg21.192
r_dihedral_angle_3_deg14.826
r_dihedral_angle_1_deg6.638
r_scangle_it5.809
r_scbond_it3.74
r_mcangle_it2.682
r_angle_refined_deg2.607
r_mcbond_it1.613
r_chiral_restr0.182
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.385
r_dihedral_angle_4_deg21.192
r_dihedral_angle_3_deg14.826
r_dihedral_angle_1_deg6.638
r_scangle_it5.809
r_scbond_it3.74
r_mcangle_it2.682
r_angle_refined_deg2.607
r_mcbond_it1.613
r_chiral_restr0.182
r_bond_refined_d0.029
r_gen_planes_refined0.016
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 Atoms1246
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms73

Software

Software
Software NamePurpose
DNAdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing