5D2B

Crystal structure of a mutated catalytic domain of Human MMP12 in complex with an hydroxamate analogue of RXP470

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	293	Protein : hMMP12 F171D at 820 micro-M + 10 milli-M AHA + 0.708 milli-M inhibitor. Precipitant : 20% PEG4000, 0.2 M TRIS pH 9.5 Cryoprotectant : 10 % diethylene glycol + 5 % glycerol + 10 % 1,2-propanediol + 5 % 1,4-dioxane + 25% PEG6000 + 0.1 M TRIS HCl pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.9	α = 90
b = 63.1	β = 90
c = 36.79	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	convex horizontal pre-focussing mirror (HPM) and a pair of focusing bimorph mirrors in Kirkpatrick-Baez (KB) configuration	2015-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.9184	SOLEIL	PROXIMA 2

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	1.2	32.453	99.6	0.1	0.089	8.78	4.6	96966	96542		-3

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	1.23	96.9		1.05	1.53	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	4GQL	1.2	32.453	1	96507	4815	99.53	0.1554	0.1544	0.1747	Random

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.719
f_angle_d	1.067
f_chiral_restr	0.07
f_plane_restr	0.006
f_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1246
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	51

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
MOLREP	phasing
MxCuBE	data collection
Coot	model building
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.