3B3X

Crystal structure of class A beta-lactamase of Bacillus licheniformis BS3 with aminocitrate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W7F	PDB ENTRY 1W7F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	7.2	293	5micro-l of a protein solution (at a concentration of 38mg/ml in 50mM NaCl, 10mM Tris buffer, pH 7.2), 4micro-l of 8% PEG 6000 in 100mM sodium aminocitrate buffer (pH 3.4) plus 1micro-l of 0.1M urea additive, equilibrated against 1ml of a 20% PEG 6000, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.665	α = 90
b = 104.71	β = 93.96
c = 63.884	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	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2005-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	63.758	82.3	0.083	0.083	7.6	1.9		17440

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	2.64	75.5		0.371	0.371	1.9	1.7	2310

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1W7F	2.5	36.47	17393	887	81.88	0.223	0.22	0.288	RANDOM	22.959

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]
		0.05	0.06		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.223
r_dihedral_angle_3_deg	19.146
r_dihedral_angle_4_deg	18.802
r_dihedral_angle_1_deg	7.666
r_scangle_it	2.964
r_scbond_it	1.857
r_angle_refined_deg	1.834
r_mcangle_it	1.354
r_mcbond_it	0.778
r_symmetry_hbond_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.223
r_dihedral_angle_3_deg	19.146
r_dihedral_angle_4_deg	18.802
r_dihedral_angle_1_deg	7.666
r_scangle_it	2.964
r_scbond_it	1.857
r_angle_refined_deg	1.834
r_mcangle_it	1.354
r_mcbond_it	0.778
r_symmetry_hbond_refined	0.316
r_nbtor_refined	0.315
r_nbd_refined	0.286
r_symmetry_vdw_refined	0.268
r_xyhbond_nbd_refined	0.226
r_chiral_restr	0.115
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3988
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	26

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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.