3F15

Crystal structure of the catalytic domain of human mmp12 complexed with the inhibitor (S)-N-(2,3-dihydroxypropyl)-4-methoxy-N-(2-nitroso-2-oxoethyl)benzenesulfonamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1M TRIS, 30% PEG 6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.557α = 90
b = 60.472β = 114.55
c = 53.859γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDOXFORD ONYX CCDmirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEOXFORD DIFFRACTION ENHANCED ULTRA1.54056

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
11.714.594.50.0390.03923.13.8157241572410.5
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)
1.71.7965.10.1140.1148.11.61575

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.714.45143011430114221000.172330.172330.170510.19048RANDOM10.307
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]
0.21-0.160.02-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.219
r_dihedral_angle_4_deg17.588
r_dihedral_angle_3_deg11.241
r_sphericity_free7.009
r_dihedral_angle_1_deg5.82
r_scangle_it2.726
r_scbond_it1.87
r_angle_refined_deg1.241
r_mcangle_it1.198
r_mcbond_it0.747
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.219
r_dihedral_angle_4_deg17.588
r_dihedral_angle_3_deg11.241
r_sphericity_free7.009
r_dihedral_angle_1_deg5.82
r_scangle_it2.726
r_scbond_it1.87
r_angle_refined_deg1.241
r_mcangle_it1.198
r_mcbond_it0.747
r_nbtor_refined0.306
r_nbd_refined0.196
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.147
r_symmetry_hbond_refined0.145
r_chiral_restr0.117
r_metal_ion_refined0.109
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1238
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms27

Software

Software
Software NamePurpose
CrysalisProdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling