5I43 | pdb_00005i43

Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate chelator water-soluble inhibitor (DC32).

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5I3M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	Protein-ligand: hMMP12 F171D E219Q 465 micro-M in 0.020 M Tris-HCl, 3 milli-M CaCl2, 0.2 M NaCl, 0.02 M acetohydroxamic acid, 10% DMSO, pH 7.5, 0.5 milli-M inhibitor (DC31). Precipitant: 40% PEG4K, 9% dioxane, 0.18 M imidazole piperidine, pH 8.5. Cryoprotectant: 40% cryomix SM2:(12.5 % ethylene glycol + 12.5 % glycerol + 12.5 % 1,2-propanediol + 25 % DMSO + 37.5 % 1,4-dioxane), 22.5% MPEG 4K, 5% dioxane, 100 mM imidazole piperidine pH 8.5.

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.03	α = 90
b = 63.66	β = 103.03
c = 79.03	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M	mirrors	2015-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97857	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.95	44.56	99.9	0.172	0.167	0.993	7.24	5.97		45366		-3	26.387

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	99.8		0.716	2.02	3.96

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5I3M	1.95	44.56	43013	2264	99.83	0.20205	0.20039	0.21	0.23323	0.24	RANDOM	27.062

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]
-1.32		0.39	-1.68		2.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.101
r_dihedral_angle_4_deg	20.364
r_dihedral_angle_3_deg	13.61
r_long_range_B_refined	8.399
r_long_range_B_other	8.177
r_dihedral_angle_1_deg	7.085
r_scangle_other	5.515
r_scbond_it	3.604
r_scbond_other	3.603
r_mcangle_other	3.45
r_mcangle_it	3.449
r_mcbond_it	2.367
r_mcbond_other	2.364
r_angle_refined_deg	1.989
r_angle_other_deg	1.073
r_chiral_restr	0.119
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.004
r_gen_planes_other	0.003
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5124
Nucleic Acid Atoms
Solvent Atoms	595
Heterogen Atoms	206

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building