Experiment: 6G0K

Crystal structure of Enterococcus faecium D63r Penicillin-Binding protein 5 (PBP5fm)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		292	Crystals were grown by the sitting-drop vapor diffusion method. Crystals were grown at 20C by mixing 1microL of PBP5fm (48 mg/ml), 2microL of reservoir (20% PEG8000 (w/v), 0.4 M Li2SO4 and 100 mM Na acetate at pH 4.5) and 0.5 microL of 0.1M ceftobiprole (kind gift of Basilea Pharmaceutica. The crystal was cryoprotected in the same buffer containing 20 % (v/v) glycerol. Crystals were soaked for 5 min in 1 microl of 0.1 M ceftobiprole before cryoprotection.

Crystal Properties
Matthews coefficient	Solvent content
3	58.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.842	α = 90
b = 128.852	β = 93.88
c = 236.25	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 PILATUS3 S 6M		2013-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9801	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.9	47.142	100	0.159	0.186	0.095	8.5	3.8		52908

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.06	100		0.793	0.93	0.481	2.5	3.8

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	2.9	47.142	1.34	52887	2689	99.93	0.2007	0.1982	0.2011	0.2468	0.2486

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	10.904
f_angle_d	1.4
f_chiral_restr	0.066
f_bond_d	0.016
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14030
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	105

Software

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