1YM1

X-ray crystallographic structure of CTX-M-9 beta-lactamase complexed with a boronic acid inhibitor (SM2)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YLJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.8	293	potassium phosphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.80

Crystal Properties
Matthews coefficient	Solvent content
1.69	27.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.12	α = 90
b = 106.717	β = 101.89
c = 47.718	γ = 90

Symmetry
Space Group	P 1 21 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 4	MIRRORS	2004-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

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	1.12	30	85.1	0.054	22.9	9.01		143714		-3

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)
	1.12	1.16	23.1		0.287	1.92

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R	1YLJ	1.12	10	133427	133427	6644	79.1	0.106	0.107	0.107	0.14	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
86	3767.81	4732.8

RMS Deviations
Key	Refinement Restraint Deviation
s_zero_chiral_vol	0.103
s_approx_iso_adps	0.074
s_non_zero_chiral_vol	0.058
s_from_restr_planes	0.037
s_similar_adp_cmpnt	0.026
s_angle_d	0.022
s_anti_bump_dis_restr	0.017
s_bond_d	0.006
s_rigid_bond_adp_cmpnt	0.001
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4211
Nucleic Acid Atoms
Solvent Atoms	861
Heterogen Atoms	64

Software

Software
Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	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.