Experiment: 3O87

Crystal structure of AmpC beta-lactamase in complex with a sulfonamide boronic acid inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KE4	PDB entry 1KE4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.7	293	1.7 M Potassium Phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.13	α = 90
b = 76.19	β = 116.16
c = 97.38	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	CCD	ADSC QUANTUM 315r		2009-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.115872	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	1.78	40	97.5	0.058	12.57	2.95	72664	72664	2	-3	19.3

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	1.78	1.88	95.7		0.455	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB entry 1KE4	1.78	38.432	1.99	72664	72662	1454	97.7	0.1888	0.188	0.1829	0.232	0.2275	Random	23.1156

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]
1.2689		4.333	-7.5774		6.3085

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.12
f_angle_d	1.355
f_chiral_restr	0.087
f_bond_d	0.011
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5431
Nucleic Acid Atoms
Solvent Atoms	519
Heterogen Atoms	41

Software

Software
Software Name	Purpose
XSCALE	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing