2WRS

Crystal Structure of the Mono-Zinc Metallo-beta-lactamase VIM-4 from Pseudomonas aeruginosa

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WHG	PDB ENTRY 2WHG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		1.55 M AMMONIUM CITRATE TRIBASIC PH 7.0 POWDER OF COMPOUND 18 IN THE DROP.

Crystal Properties
Matthews coefficient	Solvent content
3.2	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.13	α = 90
b = 45.67	β = 105.41
c = 105.03	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	ADSC CCD		2008-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	2.75	50	98.8	0.08	14.03	3.6		16118			42.096

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	2.79	2.96	96.2		0.39	3.43	3.6

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 2WHG	2.79	43.27	15312	806	100	0.20134	0.19861	0.25318	RANDOM	38.177

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]
0.57		0.13	-0.35		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.338
r_dihedral_angle_3_deg	20.277
r_dihedral_angle_4_deg	18.373
r_dihedral_angle_1_deg	7.412
r_sphericity_free	6.572
r_scangle_it	4.115
r_scbond_it	2.486
r_sphericity_bonded	2.361
r_mcangle_it	2.09
r_angle_refined_deg	1.794
r_rigid_bond_restr	1.629
r_mcbond_it	1.162
r_angle_other_deg	0.984
r_chiral_restr	0.114
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3454
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing