2GMN

Crystal structure of BJP-1, a subclass B3 metallo-beta-lactamase of Bradyrhizobium japonicum

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	0.1M Tris, 0.4M Na acetate, 40% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.501	α = 78.92
b = 44.773	β = 89.51
c = 76.966	γ = 61.91

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	100	CCD	ADSC QUANTUM 315		2005-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.281302	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.4	38.576	91				87661

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.48	77.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.4	38.58	79603	79603	8006	100	0.1797	0.1797	0.17633	0.21322	RANDOM	16.071

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]
-0.28	-0.05	-0.09	0.27	0.05	0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.946
r_dihedral_angle_4_deg	13.595
r_dihedral_angle_3_deg	12.725
r_dihedral_angle_1_deg	5.41
r_sphericity_free	2.972
r_sphericity_bonded	2.912
r_scangle_it	2.681
r_scbond_it	1.82
r_mcangle_it	1.274
r_angle_refined_deg	1.163
r_rigid_bond_restr	1.073
r_mcbond_it	0.823
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.187
r_xyhbond_nbd_refined	0.109
r_symmetry_hbond_refined	0.102
r_chiral_restr	0.073
r_metal_ion_refined	0.046
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4038
Nucleic Acid Atoms
Solvent Atoms	713
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
CCP4	data scaling
SHELXD	phasing
SHARP	phasing