3LK8 | pdb_00003lk8

Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor paramethoxy-sulfonyl-glycine hydroxamate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y93

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	289	0.1 M Tris-HCl, 30% PEG 6000, 200 mM AHA, 1.0 M LiCl2 , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.708	α = 90
b = 60.251	β = 115.16
c = 54.144	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	OXFORD ONYX CCD	mirrors	2005-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION ENHANCE ULTRA

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.8	25.81	90.6	0.034	0.034	27.2	2.9	12682	12682			9.95

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)	Redundancy	Number Unique Reflections (All)
	1.8	1.9	48.2		0.057	0.057	13.8	1.7	966

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1Y93	1.8	25.81	11546	11546	1134	100	0.17081	0.17081	0.16805	0.1676	0.19965	0.1985	RANDOM	9.595

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]
-0.01		-0.13	0.12		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.842
r_dihedral_angle_3_deg	12.451
r_dihedral_angle_4_deg	10.714
r_dihedral_angle_1_deg	6
r_scangle_it	3.021
r_scbond_it	2.06
r_mcangle_it	1.232
r_angle_refined_deg	1.202
r_mcbond_it	0.803
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.842
r_dihedral_angle_3_deg	12.451
r_dihedral_angle_4_deg	10.714
r_dihedral_angle_1_deg	6
r_scangle_it	3.021
r_scbond_it	2.06
r_mcangle_it	1.232
r_angle_refined_deg	1.202
r_mcbond_it	0.803
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.22
r_nbd_refined	0.197
r_symmetry_hbond_refined	0.131
r_metal_ion_refined	0.119
r_xyhbond_nbd_refined	0.105
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1238
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	22

Software

Software
Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.