5I3M | pdb_00005i3m

Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated thiourea-linked carboxylate zinc-chelator water-soluble inhibitor (DC31).

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5I2Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	Protein-ligand: hMMP12 F67D E219Q 465 micro-M, 0.02M acetohydroxamic acid 0.5 milli-M inhibitor (DC31) 10% DMSO. Precipitant: 32.4% PEG 4K, 8% dioxane, 0.2M imidazole piperidine, pH 8.5. Cryoprotectant: 40% cryomix:(12.5 % diethylene glycol + 12.5 % glycerol + 12.5 % 1,2-propanediol + 25 % DMSO + 25 % 1,4-dioxane) 12% PEG 4K, 10% Dioxane, 0.1 M imidazole piperidine pH 8.5.

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.72	α = 90
b = 63.14	β = 103.09
c = 78.92	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	2.17	48.79	99.3	0.1	0.096	0.997	9.44	4.34		32560		-3	33.956

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	2.17	2.23	98.9		0.523	3.06	3.73

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	5I2Z	2.17	48.79	30719	1617	99.36	0.2085	0.20615	0.22	0.25324	0.26	RANDOM	36.572

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]
-1.53		0.98	-3.8		4.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.216
r_dihedral_angle_4_deg	17.818
r_dihedral_angle_3_deg	12.398
r_long_range_B_refined	8.183
r_long_range_B_other	8.023
r_dihedral_angle_1_deg	6.907
r_scangle_other	5.652
r_mcangle_other	4.229
r_mcangle_it	4.228
r_scbond_it	3.68
r_scbond_other	3.679
r_mcbond_it	2.939
r_mcbond_other	2.938
r_angle_refined_deg	1.904
r_angle_other_deg	1.054
r_chiral_restr	0.116
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.004
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	4936
Nucleic Acid Atoms
Solvent Atoms	430
Heterogen Atoms	60

Software

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