6C89

NDM-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements for the Hydrolysis of Penicillin versus Carbapenem Antibiotics

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	0.2 M LiCl, 0.1 M HEPES, pH7.0, 20% (w/v) PEG6000

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.167	α = 92.23
b = 68.861	β = 77.026
c = 68.441	γ = 91.84

Symmetry
Space Group	P 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		2017-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1	ALS	8.2.1

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	1.75	48.668	91.07	0.053	17.6	2.3		75377			16.0102224723

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	1.75	1.813	54.76		0.325		2.2

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	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3Q6X	1.75006148726	37.2364552136	1.96361990839	75370	3746	91.0727663791	0.158241721583	0.156087511804	0.19952021866	19.4899005082

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	11.9981202544
f_angle_d	0.767076571585
f_chiral_restr	0.0531110621711
f_bond_d	0.00546008292878
f_plane_restr	0.00467596668114

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6818
Nucleic Acid Atoms
Solvent Atoms	675
Heterogen Atoms	26

Software

Software
Software Name	Purpose
phenix.refine	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

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.