6EOX | pdb_00006eox

Crystal structure of MMP12 in complex with carboxylic inhibitor LP165.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4H76

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	Drop: 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 coefficient	Solvent content
2.11	41.76

Crystal Data

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

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 315r	2nd mirror Zerodur with Pt coating	2010-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.979696	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	49	79.7	0.999	14.42	4.14		28894		-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)	Redundancy	Number Unique Reflections (All)
1	1.3	1.38	31.8		1.31	0.343	1.02	3.68

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	4H76	1.3	48.59	26772	1996	79.7	0.145	0.142	0.15	0.179	0.19	RANDOM	18.43

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	-0.39		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.86
r_sphericity_free	21.923
r_dihedral_angle_4_deg	18.752
r_dihedral_angle_3_deg	13.302
r_sphericity_bonded	7.583
r_rigid_bond_restr	6.98
r_dihedral_angle_1_deg	5.775
r_long_range_B_refined	3.854
r_long_range_B_other	3.597
r_scangle_other	3.312
r_scbond_it	2.9
r_scbond_other	2.899
r_mcangle_it	2.481
r_mcangle_other	2.481
r_mcbond_it	2.147
r_mcbond_other	2.135
r_angle_other_deg	1.936
r_angle_refined_deg	1.649
r_chiral_restr	0.113
r_bond_refined_d	0.072
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.002
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 Atoms	Number
Protein Atoms	1238
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	32

Software

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