1KR3 | pdb_00001kr3

Crystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZNB	native CfiA (1ZNB)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	32% PEG1000, 0.1M MES, 10microM ZnCl2, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.8	α = 92.8
b = 44.2	β = 95.3
c = 58.5	γ = 98

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	298	AREA DETECTOR	SIEMENS	Ni-filtered	1997-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	SIEMENS	1.542

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.5	29	75	0.092	0.092	9.3	1.9	15937	15937		2	20.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.66	56		0.23	0.23	2.5	1.9	1400

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	native CfiA (1ZNB)	2.5	29.07	10526	10526	1082	73.7	0.152	0.152	0.152	0.222	RANDOM	25.7

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]
0.72	-0.67	0.66	-2.77	1.89	2.05

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.1
c_scangle_it	5.65
c_scbond_it	4.11
c_mcangle_it	3.86
c_mcbond_it	2.54
c_angle_deg	2
c_improper_angle_d	1.17
c_bond_d	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3484
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	52

Software

Software
Software Name	Purpose
X-GEN	data scaling
X-GEN	data reduction
AMoRE	phasing
CNX	refinement

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.