3I15 | pdb_00003i15

Cobalt-substituted metallo-beta-lactamase from Bacillus cereus: residue Cys168 fully oxidized

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	293	0.1 M Sodium cacodylate, 0.1 M Sodium tartrate, 18% PEG 3350, 40 mM CoSO4, 1 mM DTT, pH 5.8, Vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.188	α = 90
b = 61.822	β = 93.24
c = 69.521	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	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2007-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	1.549	40.291	91.3	0.049	0.049	9.129	3.6		30132

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)
	1.54	1.63	77.8		0.363	0.363	2.1	3.2	3764

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	THROUGHOUT	1.55	40.29	30132	1524	92.21	0.153	0.151	0.1878	0.186	0.2179	RANDOM	18.112

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]
-0.22		-0.58	1.32		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.208
r_dihedral_angle_4_deg	15.153
r_dihedral_angle_3_deg	12.162
r_sphericity_free	11.234
r_dihedral_angle_1_deg	6.696
r_scangle_it	4.577
r_scbond_it	2.868
r_mcangle_it	1.883
r_angle_refined_deg	1.784
r_angle_other_deg	1.619

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.208
r_dihedral_angle_4_deg	15.153
r_dihedral_angle_3_deg	12.162
r_sphericity_free	11.234
r_dihedral_angle_1_deg	6.696
r_scangle_it	4.577
r_scbond_it	2.868
r_mcangle_it	1.883
r_angle_refined_deg	1.784
r_angle_other_deg	1.619
r_mcbond_it	1.096
r_mcbond_other	0.316
r_chiral_restr	0.128
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1647
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
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.