5A93

293K Joint X-ray Neutron with Cefotaxime: EXPLORING THE MECHANISM OF BETA-LACTAM RING PROTONATION IN THE CLASS A BETA-LACTAMASE ACYLATION MECHANISM USING NEUTRON AND X-RAY CRYSTALLOGRAPHY

NEUTRON DIFFRACTION - X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XR0	PDB ENTRY 2XR0PDB ENTRY 2XR0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.9
2		6.1

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.91
2.73	54.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.315	α = 90
b = 73.315	β = 90
c = 98.87	γ = 120

Symmetry
Space Group	P 32 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	293	IMAGE PLATE	RIGAKU RAXIS IV++		2010-04-05	M	SINGLE WAVELENGTH
2	2	neutron	293	SNS ANGER CAMERA	ORNL ANGER CAMERA	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E DW	1.54
2	NUCLEAR REACTOR	ORNL Spallation Neutron Source BEAMLINE MANDI	3.0	ORNL Spallation Neutron Source	MANDI

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (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	1.6	19.5	99.5	0.077						6.1	6.8		41094
2	2.2	15.21	71.4	0.171	0.17					9.4	3.9		11803

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.68		0.297						2.8	5.8
2	2.2	2.28		0.252						3.9	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	1.598	19.503		1.34		41055	2066	99.53		0.1345	0.1334	0.22	0.1562	0.24
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.2	15.03				11579	574	72.26		0.218	0.2171		0.2363

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	19.221
f_angle_d	1.248
f_chiral_restr	0.087
f_bond_d	0.012
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1961
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	51

Software

Software
Software Name	Purpose
CNS	phasing
PHENIX	refinement
Mantid	data reduction
Mantid	data scaling
d*TREK	data reduction
d*TREK	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.