Experiment: 9S6B

Aeropyrum pernix acylaminoacyl peptidase co-crystallized with meropenem.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O4H	A functional dimer of monomers in open and closed conformations was used as model after removal of the segments 444-446, 523-525 and 555-557.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	Reservoir: 0.45mM EDTA, 33mM sodium acetate buffer pH=5.0, 1.2% PEG Mw 4000; Protein solution: 0.24 mM in 20mM Tris pH=8.0, Meropenem solution: 62.5mM in methanol. Drop content: reservoir/protein/meropenem solutions= 1/1/0.5 volume ratio. Crystals were soaked in 30%w/w HbPG solurion saturated with meropenem.

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.042	α = 105.51
b = 98.283	β = 103.19
c = 98.902	γ = 100.39

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	PIXEL	DECTRIS PILATUS 6M-F		2016-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.3	40	98.1	0.081	0.997	9.36	3		105834			62.56

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36	95		1.022	0.502	1.05

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.3	39.22	1.95	105790	2101	98.21	0.1974	0.1968	0.1968	0.2286	0.2287	69.92

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	11.6851
f_angle_d	0.5621
f_chiral_restr	0.0442
f_plane_restr	0.0042
f_bond_d	0.0025

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16639
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	23

Software

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