5B5O

Crystal structure of the catalytic domain of MMP-13 complexed with N-phenyl-4-((4H-1,2,4-triazol-3-ylsulfanyl)methyl)-1,3-thiazol-2-amine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	100mM TrisHCl, 1500mM ammonium formate, 10.4% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.409	α = 90
b = 36.06	β = 131.09
c = 95.948	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		2012-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.97645	ALS	5.0.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.2	50	94.9	0.051	15.5	3		104586

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	1.2	1.22	60.4		0.363		1.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	830C	1.2	33.75	104585	5238	94.9	0.1648	0.1638	0.1854	RANDOM	15.5145

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]
0.56		0.24	-0.19		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.51
r_dihedral_angle_4_deg	22.217
r_dihedral_angle_3_deg	11.104
r_dihedral_angle_1_deg	6.081
r_scangle_it	3.644
r_scbond_it	2.568
r_mcangle_it	1.921
r_angle_refined_deg	1.224
r_mcbond_it	1.08
r_nbtor_refined	0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.51
r_dihedral_angle_4_deg	22.217
r_dihedral_angle_3_deg	11.104
r_dihedral_angle_1_deg	6.081
r_scangle_it	3.644
r_scbond_it	2.568
r_mcangle_it	1.921
r_angle_refined_deg	1.224
r_mcbond_it	1.08
r_nbtor_refined	0.314
r_symmetry_hbond_refined	0.202
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.157
r_xyhbond_nbd_refined	0.118
r_metal_ion_refined	0.098
r_chiral_restr	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2645
Nucleic Acid Atoms
Solvent Atoms	555
Heterogen Atoms	52

Software

Software
Software Name	Purpose
SCALEPACK	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
MOLREP	phasing
HKL	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.