2NZF

Structure of beta-lactamase II from Bacillus cereus. R121H, C221S double mutant. Space group C2.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BC2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	295	0.1 M sodium cacodylate, 60 mM sodium tartrate, 18% PEG 3350, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.587	α = 90
b = 61.156	β = 93.11
c = 68.634	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	MAR CCD 165 mm		2006-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1		LNLS	D03B-MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.28	50	98.3	0.059	14.8	6.4		9968

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.28	2.35	83		0.17	9.7	2.8

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	1bc2	2.28	68.52	9968	478	99.75	0.167	0.163	0.238	RANDOM	24.092

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]
-0.42		-0.72	0.62		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.114
r_dihedral_angle_4_deg	18.471
r_dihedral_angle_3_deg	15.974
r_dihedral_angle_1_deg	7.322
r_scangle_it	4.835
r_scbond_it	3.045
r_angle_refined_deg	2.034
r_mcangle_it	1.876
r_mcbond_it	1.075
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.114
r_dihedral_angle_4_deg	18.471
r_dihedral_angle_3_deg	15.974
r_dihedral_angle_1_deg	7.322
r_scangle_it	4.835
r_scbond_it	3.045
r_angle_refined_deg	2.034
r_mcangle_it	1.876
r_mcbond_it	1.075
r_nbtor_refined	0.315
r_nbd_refined	0.217
r_symmetry_vdw_refined	0.214
r_xyhbond_nbd_refined	0.181
r_symmetry_hbond_refined	0.156
r_chiral_restr	0.127
r_metal_ion_refined	0.04
r_bond_refined_d	0.021
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1666
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	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.