5B5P

Crystal structure of the catalytic domain of MMP-13 complexed with 4-oxo-N-(3-(2-(1H-1,2,4-triazol-3-ylsulfanyl)ethoxy)benzyl)-3,4-dihydroquinazoline-2-carboxamide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	100mM TrisHCl, 1000mM ammonium formate, 15.3% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.798	α = 90
b = 36.281	β = 130.14
c = 96.382	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		2012-08-03	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	1.6	50	97.1	0.074	13.8	3.8		46398

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	1.6	1.63	68.5		0.443		2.8

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	5B5O	1.6	36.84	46396	2346	96.96	0.175	0.1733	0.208	RANDOM	24.4984

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]
0.93			-1.16		1.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.218
r_dihedral_angle_4_deg	19.88
r_dihedral_angle_3_deg	12.565
r_dihedral_angle_1_deg	5.549
r_scangle_it	4.609
r_scbond_it	3.247
r_mcangle_it	2.183
r_mcbond_it	1.423
r_angle_refined_deg	1.181
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.218
r_dihedral_angle_4_deg	19.88
r_dihedral_angle_3_deg	12.565
r_dihedral_angle_1_deg	5.549
r_scangle_it	4.609
r_scbond_it	3.247
r_mcangle_it	2.183
r_mcbond_it	1.423
r_angle_refined_deg	1.181
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.202
r_nbd_refined	0.187
r_metal_ion_refined	0.182
r_symmetry_vdw_refined	0.152
r_xyhbond_nbd_refined	0.101
r_chiral_restr	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2648
Nucleic Acid Atoms
Solvent Atoms	398
Heterogen Atoms	70

Software

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