3LVZ

New refinement of the crystal structure of BJP-1, a subclass B3 metallo-beta-lactamase of Bradyrhizobium japonicum

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	30-35% PEG 4000, 0.5M sodium acetate, 5mM ZnCl2 pH 8.0-8.5, 0.1M TrisHCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.67

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 315r	mirrors	2005-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.2813	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.4	38.58	91	0.06	7.1	3.7	87611	87611		1.6	14.05

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.4	1.48	77.2		0.336	1.8	3.5	10821

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	SAD	THROUGHOUT	1.4	32.24	2	79602	8006	100	0.16503	0.16217	0.19348	RANDOM	9.088

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.152
r_dihedral_angle_4_deg	19.99
r_dihedral_angle_3_deg	12.124
r_dihedral_angle_1_deg	5.9
r_scangle_it	4.627
r_scbond_it	2.993
r_angle_refined_deg	2.204
r_mcangle_it	2.046
r_mcbond_it	1.273
r_angle_other_deg	1.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.152
r_dihedral_angle_4_deg	19.99
r_dihedral_angle_3_deg	12.124
r_dihedral_angle_1_deg	5.9
r_scangle_it	4.627
r_scbond_it	2.993
r_angle_refined_deg	2.204
r_mcangle_it	2.046
r_mcbond_it	1.273
r_angle_other_deg	1.093
r_mcbond_other	0.446
r_chiral_restr	0.131
r_bond_refined_d	0.026
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4109
Nucleic Acid Atoms
Solvent Atoms	482
Heterogen Atoms	6

Software

Software
Software Name	Purpose
ADSC	data collection
SHARP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.