Experiment: 3TVC

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QJ2	3QJ2 catalytic domain only (Chain A)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	PROTEIN-INHIBITOR SOLUTION: MMP13 AT 20 MG/ML CO-CRYSTALLIZED WITH E3P AT 1.1 MILLI-M. RESERVOIR SOLUTION: 17.5% PEG 20K, 0.1 M MES, 0.02 M NACL. CRYOPROTECTANT: 5% DIETHYLENE GLYCOL, 5% ETHYLENE GLYCOL, 5% MPD, 5% PROPYLENE GLYCOL, 5% DMSO, 5% GLYCEROL, 0.005 M 3-(-PYRIDINIO)-1-PROPANESULFONATE, 10% PEG 20K, 0.033 M SODIUM ACETATE, 0.033 M ADA, 0.033 M BICINE, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.303	α = 90
b = 85.16	β = 90
c = 40.916	γ = 90

Symmetry
Space Group	P 21 21 2

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	bent cylindrical mirror	2011-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.972420	ESRF	ID23-1

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	2.43	85.1	96.9	0.29	0.31	10.6	7.21	8412	8151			35.49

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	2.43	2.59	87.4		1.399	1.29	2.81	6.63	1231

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	3QJ2 catalytic domain only (Chain A)	2.43	40.916	1.34	8377	8127	369	97.02	0.1654	0.1622	0.2341	RANDOM	24.782

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]
-2.7543			1.2548		1.4995

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	21.949
f_angle_d	1.121
f_chiral_restr	0.083
f_bond_d	0.008
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1347
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	58

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	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.