2WHG

Crystal Structure of the Di-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	1KO3	PDB ENTRY 1KO3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		1.55 M AMMONIUM CITRATE TRIBASIC PH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.3	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.39	α = 90
b = 46.22	β = 105.24
c = 105.99	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		2008-03-07	M	SINGLE WAVELENGTH

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

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	1.9	47.3	98.6	0.1	8.92	3.6		52283			26.59

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	1.9	2	95.7		0.44	2.59	3.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1KO3	1.9	47.3	49667	2615	100	0.202	0.2	0.2	0.254	0.26	RANDOM	26.52

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]
1.67		-0.4	-1.02		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.772
r_dihedral_angle_4_deg	17.679
r_dihedral_angle_3_deg	16.411
r_sphericity_free	7.259
r_dihedral_angle_1_deg	6.337
r_sphericity_bonded	3.975
r_scangle_it	3.362
r_scbond_it	2.278
r_mcangle_it	1.579
r_rigid_bond_restr	1.48
r_angle_refined_deg	1.424
r_mcbond_it	1.023
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.231
r_symmetry_vdw_refined	0.225
r_nbd_refined	0.192
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.099
r_metal_ion_refined	0.078
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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	435
Heterogen Atoms	30

Software

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