5O7N | pdb_00005o7n

Beta-lactamase VIM-2 in complex with (2R)-1-(2-Benzyl-3-mercaptopropanoyl)piperidine-2-carboxylic acid

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	290.15	The VIM-2 in crystallization buffer (50 mM Tris/HCl pH 7.2, 100 uM ZnCl2 and 150 mM NaCl) was concentrated to 11,4 mg/mL, before 5 % Glycerol was added and the protein was flash frozen in liquid nitrogen. For crystallisation the thrawed protein solutions was mixed with precipitation solution (34% PEG3350, 0,25 M Mg formate, 5 mM BME + 2.5% of a 1M DMSO inhibitor stock in the drop) in differant ratios. As reservoir precipitation solution without inhibitor was used.

Crystal Properties
Matthews coefficient	Solvent content
1.84	32.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.989	α = 90
b = 79.308	β = 130.45
c = 67.645	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	PIXEL	DECTRIS EIGER X 4M		2016-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.5	55.5074	99.13	0.07561	0.04672	0.998	10.74	3.6		128072			13.97

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.554	99.62		0.5409	0.338	0.763	2.17	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	SAD	FREE R-VALUE	1.5	55.5074	128064	3573	99.13	0.1874	0.1869	0.19	0.2112	0.21	Random selection	18.2

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	19.994
f_angle_d	0.936
f_chiral_restr	0.065
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3489
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	82

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
AutoSol	phasing
XSCALE	data scaling
PHASER	phasing

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.